diff --git a/.travis.yml b/.travis.yml index d4ea00e6e4e..a3b305de373 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,6 +6,8 @@ python: 2.7 env: - CHUNK=0 - CHUNK=1 + - CHUNK=2 + - CHUNK=3 before_install: - export GALAXY_REPO=https://github.com/galaxyproject/galaxy @@ -32,7 +34,7 @@ install: planemo ci_find_repos --exclude_from .tt_blacklist \ --exclude packages --exclude data_managers \ --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \ - --chunk_count 2 --chunk "${CHUNK}" \ + --chunk_count 4 --chunk "${CHUNK}" \ --output changed_repositories_chunk.list - cat changed_repositories_chunk.list diff --git a/tool_collections/kraken/README.rst b/tool_collections/kraken/README.rst new file mode 100644 index 00000000000..4acd6859923 --- /dev/null +++ b/tool_collections/kraken/README.rst @@ -0,0 +1,92 @@ +Introduction +============ + +`Kraken `__ is a taxonomic sequence +classifier that assigns taxonomic labels to short DNA reads. It does +this by examining the :math:`k`-mers within a read and querying a +database with those :math:`k`-mers. This database contains a mapping of +every :math:`k`-mer in +`Kraken `__'s genomic library to +the lowest common ancestor (LCA) in a taxonomic tree of all genomes that +contain that :math:`k`-mer. The set of LCA taxa that correspond to the +:math:`k`-mers in a read are then analyzed to create a single taxonomic +label for the read; this label can be any of the nodes in the taxonomic +tree. `Kraken `__ is designed to be +rapid, sensitive, and highly precise. Our tests on various real and +simulated data have shown +`Kraken `__ to have sensitivity +slightly lower than Megablast with precision being slightly higher. On a +set of simulated 100 bp reads, +`Kraken `__ processed over 1.3 +million reads per minute on a single core in normal operation, and over +4.1 million reads per minute in quick operation. + +The latest released version of Kraken will be available at the `Kraken +website `__, and the latest updates +to the Kraken source code are available at the `Kraken GitHub +repository `__. + +If you use `Kraken `__ in your +research, please cite the `Kraken +paper `__. Thank you! + +System Requirements +=================== + +Note: Users concerned about the disk or memory requirements should read +the paragraph about MiniKraken, below. + +- **Disk space**: Construction of Kraken's standard database will + require at least 160 GB of disk space. Customized databases may + require more or less space. Disk space used is linearly proportional + to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's + default database contains just under 6 billion (6e9) distinct + :math:`k`-mers. + + In addition, the disk used to store the database should be + locally-attached storage. Storing the database on a network + filesystem (NFS) partition can cause Kraken's operation to be very + slow, or to be stopped completely. As NFS accesses are much slower + than local disk accesses, both preloading and database building will + be slowed by use of NFS. + +- **Memory**: To run efficiently, Kraken requires enough free memory to + hold the database in RAM. While this can be accomplished using a + ramdisk, Kraken supplies a utility for loading the database into RAM + via the OS cache. The default database size is 75 GB (as of Feb. + 2015), and so you will need at least that much RAM if you want to + build or run with the default database. + +- **Dependencies**: Kraken currently makes extensive use of Linux + utilities such as sed, find, and wget. Many scripts are written using + the Bash shell, and the main scripts are written using Perl. Core + programs needed to build the database and run the classifier are + written in C++, and need to be compiled using g++. Multithreading is + handled using OpenMP. Downloads of NCBI data are performed by wget + and in some cases, by rsync. Most Linux systems that have any sort of + development package installed will have all of the above listed + programs and libraries available. + + Finally, if you want to build your own database, you will need to + install the + `Jellyfish `__ + :math:`k`-mer counter. Note that Kraken only supports use of + Jellyfish version 1. Jellyfish version 2 is not yet compatible with + Kraken. + +- **Network connectivity**: Kraken's standard database build and + download commands expect unfettered FTP and rsync access to the NCBI + FTP server. If you're working behind a proxy, you may need to set + certain environment variables (such as ``ftp_proxy`` or + ``RSYNC_PROXY``) in order to get these commands to work properly. + +- **MiniKraken**: To allow users with low-memory computing environments + to use Kraken, we supply a reduced standard database that can be + downloaded from the Kraken web site. When Kraken is run with a + reduced database, we call it MiniKraken. + + The database we make available is only 4 GB in size, and should run + well on computers with as little as 8 GB of RAM. Disk space required + for this database is also only 4 GB. + + diff --git a/tool_collections/kraken/database.idx b/tool_collections/kraken/database.idx new file mode 100644 index 00000000000..1a06ff64f27 Binary files /dev/null and b/tool_collections/kraken/database.idx differ diff --git a/tool_collections/kraken/database.kdb b/tool_collections/kraken/database.kdb new file mode 100644 index 00000000000..35447d3771e Binary files /dev/null and b/tool_collections/kraken/database.kdb differ diff --git a/tool_collections/kraken/kraken/.shed.yml b/tool_collections/kraken/kraken/.shed.yml new file mode 100644 index 00000000000..00699d0b194 --- /dev/null +++ b/tool_collections/kraken/kraken/.shed.yml @@ -0,0 +1,16 @@ +categories: +- Metagenomics +description: Kraken for taxonomic designation. +homepage_url: http://ccb.jhu.edu/software/kraken/ +long_description: | + Kraken is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence alignment + or machine learning techniques that were quite slow, leading to the development + of less sensitive but much faster abundance estimation programs. Kraken aims to + achieve high sensitivity and high speed by utilizing exact alignments of k-mers + and a novel classification algorithm. +name: kraken +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ +type: unrestricted diff --git a/tool_collections/kraken/kraken/README.rst b/tool_collections/kraken/kraken/README.rst new file mode 120000 index 00000000000..89a0106941f --- /dev/null +++ b/tool_collections/kraken/kraken/README.rst @@ -0,0 +1 @@ +../README.rst \ No newline at end of file diff --git a/tool_collections/kraken/kraken/kraken.xml b/tool_collections/kraken/kraken/kraken.xml new file mode 100644 index 00000000000..10e5f3039e7 --- /dev/null +++ b/tool_collections/kraken/kraken/kraken.xml @@ -0,0 +1,149 @@ + + + + assign taxonomic labels to sequencing reads + + + macros.xml + + + + + "${output}" + ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (split_reads) + + + (split_reads) + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/kraken/kraken/macros.xml b/tool_collections/kraken/kraken/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/kraken/kraken/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/kraken/kraken/test-data/kraken_test1.fa b/tool_collections/kraken/kraken/test-data/kraken_test1.fa new file mode 100644 index 00000000000..dfc5125a6a6 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/kraken_test1.fa @@ -0,0 +1,70 @@ +>gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence +CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAAC +TCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCA +ATGAAGCGGCGCACGAAAAACGCGAAAGCGT + +>gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence +CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGG +AGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAA +GCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT + +>gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence +TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGA +AGCGGCGCACGAAAAACGCGAAAGCGT + +>gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence +GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTC +ACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAA +TCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCA +TCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACC +TAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTG +TTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACC +GGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTAT +TGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTC +TGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCA +GCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAA +CAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTT +TTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGT +TGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCAT +GAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATA +GGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATG +AACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCG +TTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAG +TGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCG +CTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTT +CAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACT +TCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCA +TCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGAT +TTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCT +GCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCT +GTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGG +TTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACA +AATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACG +CGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGT +AATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCG +TGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCAT +TCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTG +CAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCT +GGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTT +TCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGG +TCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTAC +CCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCA +GGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTC +TACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAA +ATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGA +TTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAA +CCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAA +CACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATG +ACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCA +GGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC +ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGG +CGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCT +TCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTC +AAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGA +TGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTAC +TGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCG +TACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTT +TTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTG +TTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACT +ACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGAT +TTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG diff --git a/tool_collections/kraken/kraken/test-data/kraken_test1_output.tab b/tool_collections/kraken/kraken/test-data/kraken_test1_output.tab new file mode 100644 index 00000000000..2aa9e1ea8d5 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/kraken_test1_output.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff --git a/tool_collections/kraken/kraken/test-data/test_database.loc b/tool_collections/kraken/kraken/test-data/test_database.loc new file mode 120000 index 00000000000..03ec4336e45 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/test_database.loc @@ -0,0 +1 @@ +../../test_database.loc \ No newline at end of file diff --git a/tool_collections/kraken/kraken/test-data/test_db/database.idx b/tool_collections/kraken/kraken/test-data/test_db/database.idx new file mode 120000 index 00000000000..9251273d383 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/test_db/database.idx @@ -0,0 +1 @@ +../../../database.idx \ No newline at end of file diff --git a/tool_collections/kraken/kraken/test-data/test_db/database.kdb b/tool_collections/kraken/kraken/test-data/test_db/database.kdb new file mode 120000 index 00000000000..64efac5ce08 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/test_db/database.kdb @@ -0,0 +1 @@ +../../../database.kdb \ No newline at end of file diff --git a/tool_collections/kraken/kraken/test-data/test_db/taxonomy/names.dmp b/tool_collections/kraken/kraken/test-data/test_db/taxonomy/names.dmp new file mode 120000 index 00000000000..f4585471fc2 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/test_db/taxonomy/names.dmp @@ -0,0 +1 @@ +../../../../names.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken/test-data/test_db/taxonomy/nodes.dmp b/tool_collections/kraken/kraken/test-data/test_db/taxonomy/nodes.dmp new file mode 120000 index 00000000000..a65d7d41f87 --- /dev/null +++ b/tool_collections/kraken/kraken/test-data/test_db/taxonomy/nodes.dmp @@ -0,0 +1 @@ +../../../../nodes.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken/tool-data/kraken_databases.loc.sample b/tool_collections/kraken/kraken/tool-data/kraken_databases.loc.sample new file mode 120000 index 00000000000..eba8983e9ea --- /dev/null +++ b/tool_collections/kraken/kraken/tool-data/kraken_databases.loc.sample @@ -0,0 +1 @@ +../../kraken_databases.loc.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken/tool_data_table_conf.xml.sample b/tool_collections/kraken/kraken/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..332baf440e9 --- /dev/null +++ b/tool_collections/kraken/kraken/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken/tool_data_table_conf.xml.test b/tool_collections/kraken/kraken/tool_data_table_conf.xml.test new file mode 120000 index 00000000000..f8050b61701 --- /dev/null +++ b/tool_collections/kraken/kraken/tool_data_table_conf.xml.test @@ -0,0 +1 @@ +../tool_data_table_conf.xml.test \ No newline at end of file diff --git a/tool_collections/kraken/kraken_databases.loc.sample b/tool_collections/kraken/kraken_databases.loc.sample new file mode 100644 index 00000000000..e69de29bb2d diff --git a/tool_collections/kraken/kraken_filter/.shed.yml b/tool_collections/kraken/kraken_filter/.shed.yml new file mode 100644 index 00000000000..37aedb65a83 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/.shed.yml @@ -0,0 +1,16 @@ +categories: +- Metagenomics +description: Kraken's confidence filter. +homepage_url: http://ccb.jhu.edu/software/kraken/ +long_description: | + Kraken is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence alignment + or machine learning techniques that were quite slow, leading to the development + of less sensitive but much faster abundance estimation programs. Kraken aims to + achieve high sensitivity and high speed by utilizing exact alignments of k-mers + and a novel classification algorithm. +name: kraken_filter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ +type: unrestricted diff --git a/tool_collections/kraken/kraken_filter/README.rst b/tool_collections/kraken/kraken_filter/README.rst new file mode 120000 index 00000000000..89a0106941f --- /dev/null +++ b/tool_collections/kraken/kraken_filter/README.rst @@ -0,0 +1 @@ +../README.rst \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/kraken-filter.xml b/tool_collections/kraken/kraken_filter/kraken-filter.xml new file mode 100644 index 00000000000..706cdb528a4 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/kraken-filter.xml @@ -0,0 +1,66 @@ + + filter classification by confidence score + + macros.xml + + + + '$filtered_output' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/kraken/kraken_filter/macros.xml b/tool_collections/kraken/kraken_filter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/test-data/kraken_filter_test1.tab b/tool_collections/kraken/kraken_filter/test-data/kraken_filter_test1.tab new file mode 100644 index 00000000000..2aa9e1ea8d5 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/kraken_filter_test1.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff --git a/tool_collections/kraken/kraken_filter/test-data/kraken_filter_test1_output.tab b/tool_collections/kraken/kraken_filter/test-data/kraken_filter_test1_output.tab new file mode 100644 index 00000000000..9050d543951 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/kraken_filter_test1_output.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 P=1.000 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 P=1.000 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 P=1.000 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 P=1.000 83333:3841 diff --git a/tool_collections/kraken/kraken_filter/test-data/kraken_test1.fa b/tool_collections/kraken/kraken_filter/test-data/kraken_test1.fa new file mode 100644 index 00000000000..dfc5125a6a6 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/kraken_test1.fa @@ -0,0 +1,70 @@ +>gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence +CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAAC +TCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCA +ATGAAGCGGCGCACGAAAAACGCGAAAGCGT + +>gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence +CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGG +AGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAA +GCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT + +>gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence +TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGA +AGCGGCGCACGAAAAACGCGAAAGCGT + +>gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence +GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTC +ACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAA +TCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCA +TCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACC +TAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTG +TTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACC +GGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTAT +TGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTC +TGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCA +GCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAA +CAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTT +TTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGT +TGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCAT +GAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATA +GGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATG +AACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCG +TTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAG +TGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCG +CTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTT +CAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACT +TCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCA +TCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGAT +TTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCT +GCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCT +GTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGG +TTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACA +AATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACG +CGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGT +AATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCG +TGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCAT +TCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTG +CAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCT +GGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTT +TCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGG +TCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTAC +CCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCA +GGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTC +TACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAA +ATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGA +TTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAA +CCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAA +CACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATG +ACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCA +GGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC +ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGG +CGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCT +TCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTC +AAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGA +TGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTAC +TGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCG +TACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTT +TTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTG +TTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACT +ACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGAT +TTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG diff --git a/tool_collections/kraken/kraken_filter/test-data/test_database.loc b/tool_collections/kraken/kraken_filter/test-data/test_database.loc new file mode 120000 index 00000000000..03ec4336e45 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/test_database.loc @@ -0,0 +1 @@ +../../test_database.loc \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/test-data/test_db/database.idx b/tool_collections/kraken/kraken_filter/test-data/test_db/database.idx new file mode 120000 index 00000000000..9251273d383 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/test_db/database.idx @@ -0,0 +1 @@ +../../../database.idx \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/test-data/test_db/database.kdb b/tool_collections/kraken/kraken_filter/test-data/test_db/database.kdb new file mode 120000 index 00000000000..64efac5ce08 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/test_db/database.kdb @@ -0,0 +1 @@ +../../../database.kdb \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/test-data/test_db/taxonomy/names.dmp b/tool_collections/kraken/kraken_filter/test-data/test_db/taxonomy/names.dmp new file mode 120000 index 00000000000..f4585471fc2 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/test_db/taxonomy/names.dmp @@ -0,0 +1 @@ +../../../../names.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/test-data/test_db/taxonomy/nodes.dmp b/tool_collections/kraken/kraken_filter/test-data/test_db/taxonomy/nodes.dmp new file mode 120000 index 00000000000..a65d7d41f87 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/test-data/test_db/taxonomy/nodes.dmp @@ -0,0 +1 @@ +../../../../nodes.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/tool-data/kraken_databases.loc.sample b/tool_collections/kraken/kraken_filter/tool-data/kraken_databases.loc.sample new file mode 120000 index 00000000000..eba8983e9ea --- /dev/null +++ b/tool_collections/kraken/kraken_filter/tool-data/kraken_databases.loc.sample @@ -0,0 +1 @@ +../../kraken_databases.loc.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/tool_data_table_conf.xml.sample b/tool_collections/kraken/kraken_filter/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..332baf440e9 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken_filter/tool_data_table_conf.xml.test b/tool_collections/kraken/kraken_filter/tool_data_table_conf.xml.test new file mode 120000 index 00000000000..f8050b61701 --- /dev/null +++ b/tool_collections/kraken/kraken_filter/tool_data_table_conf.xml.test @@ -0,0 +1 @@ +../tool_data_table_conf.xml.test \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/.shed.yml b/tool_collections/kraken/kraken_report/.shed.yml new file mode 100644 index 00000000000..344d485e952 --- /dev/null +++ b/tool_collections/kraken/kraken_report/.shed.yml @@ -0,0 +1,16 @@ +categories: +- Metagenomics +description: Kraken report. +homepage_url: http://ccb.jhu.edu/software/kraken/ +long_description: | + Kraken is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence alignment + or machine learning techniques that were quite slow, leading to the development + of less sensitive but much faster abundance estimation programs. Kraken aims to + achieve high sensitivity and high speed by utilizing exact alignments of k-mers + and a novel classification algorithm. +name: kraken_report +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ +type: unrestricted diff --git a/tool_collections/kraken/kraken_report/README.rst b/tool_collections/kraken/kraken_report/README.rst new file mode 120000 index 00000000000..89a0106941f --- /dev/null +++ b/tool_collections/kraken/kraken_report/README.rst @@ -0,0 +1 @@ +../README.rst \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/kraken-mpa-report.xml b/tool_collections/kraken/kraken_report/kraken-mpa-report.xml new file mode 100644 index 00000000000..8b24450c4ef --- /dev/null +++ b/tool_collections/kraken/kraken_report/kraken-mpa-report.xml @@ -0,0 +1,81 @@ + + + view report of classification for multiple samples + + macros.xml + + + + '$output_report' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/kraken/kraken_report/kraken-report.xml b/tool_collections/kraken/kraken_report/kraken-report.xml new file mode 100644 index 00000000000..062c09897c4 --- /dev/null +++ b/tool_collections/kraken/kraken_report/kraken-report.xml @@ -0,0 +1,56 @@ + + view sample report of a classification + + + macros.xml + + + + '$output_report' + ]]> + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/kraken/kraken_report/macros.xml b/tool_collections/kraken/kraken_report/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/kraken/kraken_report/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_input1.tab b/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_input1.tab new file mode 100644 index 00000000000..2aa9e1ea8d5 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_input1.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff --git a/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_input2.tab b/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_input2.tab new file mode 100644 index 00000000000..2aa9e1ea8d5 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_input2.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff --git a/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_test1_output.tab b/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_test1_output.tab new file mode 100644 index 00000000000..ac03dc264ef --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/kraken_mpa_report_test1_output.tab @@ -0,0 +1,8 @@ +#Sample ID kraken_mpa_report_input1.tab kraken_mpa_report_input2.tab +d__Bacteria 4 4 +d__Bacteria|p__Proteobacteria 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 4 4 diff --git a/tool_collections/kraken/kraken_report/test-data/kraken_report_test1.tab b/tool_collections/kraken/kraken_report/test-data/kraken_report_test1.tab new file mode 100644 index 00000000000..2aa9e1ea8d5 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/kraken_report_test1.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff --git a/tool_collections/kraken/kraken_report/test-data/kraken_report_test1_output.tab b/tool_collections/kraken/kraken_report/test-data/kraken_report_test1_output.tab new file mode 100644 index 00000000000..1fcaa3e8cd7 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/kraken_report_test1_output.tab @@ -0,0 +1,11 @@ + 0.00 0 0 U 0 unclassified +100.00 4 0 - 1 root +100.00 4 0 - 131567 cellular organisms +100.00 4 0 D 2 Bacteria +100.00 4 0 P 1224 Proteobacteria +100.00 4 0 C 1236 Gammaproteobacteria +100.00 4 0 O 91347 Enterobacteriales +100.00 4 0 F 543 Enterobacteriaceae +100.00 4 0 G 561 Escherichia +100.00 4 0 S 562 Escherichia coli +100.00 4 4 - 83333 Escherichia coli K-12 diff --git a/tool_collections/kraken/kraken_report/test-data/test_database.loc b/tool_collections/kraken/kraken_report/test-data/test_database.loc new file mode 120000 index 00000000000..03ec4336e45 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/test_database.loc @@ -0,0 +1 @@ +../../test_database.loc \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/test-data/test_db/database.idx b/tool_collections/kraken/kraken_report/test-data/test_db/database.idx new file mode 120000 index 00000000000..9251273d383 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/test_db/database.idx @@ -0,0 +1 @@ +../../../database.idx \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/test-data/test_db/database.kdb b/tool_collections/kraken/kraken_report/test-data/test_db/database.kdb new file mode 120000 index 00000000000..64efac5ce08 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/test_db/database.kdb @@ -0,0 +1 @@ +../../../database.kdb \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/test-data/test_db/taxonomy/names.dmp b/tool_collections/kraken/kraken_report/test-data/test_db/taxonomy/names.dmp new file mode 120000 index 00000000000..f4585471fc2 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/test_db/taxonomy/names.dmp @@ -0,0 +1 @@ +../../../../names.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/test-data/test_db/taxonomy/nodes.dmp b/tool_collections/kraken/kraken_report/test-data/test_db/taxonomy/nodes.dmp new file mode 120000 index 00000000000..a65d7d41f87 --- /dev/null +++ b/tool_collections/kraken/kraken_report/test-data/test_db/taxonomy/nodes.dmp @@ -0,0 +1 @@ +../../../../nodes.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/tool-data/kraken_databases.loc.sample b/tool_collections/kraken/kraken_report/tool-data/kraken_databases.loc.sample new file mode 120000 index 00000000000..eba8983e9ea --- /dev/null +++ b/tool_collections/kraken/kraken_report/tool-data/kraken_databases.loc.sample @@ -0,0 +1 @@ +../../kraken_databases.loc.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/tool_data_table_conf.xml.sample b/tool_collections/kraken/kraken_report/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..332baf440e9 --- /dev/null +++ b/tool_collections/kraken/kraken_report/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken_report/tool_data_table_conf.xml.test b/tool_collections/kraken/kraken_report/tool_data_table_conf.xml.test new file mode 120000 index 00000000000..f8050b61701 --- /dev/null +++ b/tool_collections/kraken/kraken_report/tool_data_table_conf.xml.test @@ -0,0 +1 @@ +../tool_data_table_conf.xml.test \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/.shed.yml b/tool_collections/kraken/kraken_translate/.shed.yml new file mode 100644 index 00000000000..6e54a30ca82 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/.shed.yml @@ -0,0 +1,16 @@ +homepage_url: http://ccb.jhu.edu/software/kraken/ +categories: +- Metagenomics +description: Kraken translate command. +long_description: | + Kraken is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence alignment + or machine learning techniques that were quite slow, leading to the development + of less sensitive but much faster abundance estimation programs. Kraken aims to + achieve high sensitivity and high speed by utilizing exact alignments of k-mers + and a novel classification algorithm. +name: kraken_translate +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_translate/ +type: unrestricted diff --git a/tool_collections/kraken/kraken_translate/README.rst b/tool_collections/kraken/kraken_translate/README.rst new file mode 120000 index 00000000000..89a0106941f --- /dev/null +++ b/tool_collections/kraken/kraken_translate/README.rst @@ -0,0 +1 @@ +../README.rst \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/kraken-translate.xml b/tool_collections/kraken/kraken_translate/kraken-translate.xml new file mode 100644 index 00000000000..44ef1375deb --- /dev/null +++ b/tool_collections/kraken/kraken_translate/kraken-translate.xml @@ -0,0 +1,61 @@ + + convert taxonomy IDs to names + + macros.xml + + + + '${translated}' + ]]> + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/kraken/kraken_translate/macros.xml b/tool_collections/kraken/kraken_translate/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/test-data/kraken_translate_test1.tab b/tool_collections/kraken/kraken_translate/test-data/kraken_translate_test1.tab new file mode 100644 index 00000000000..2aa9e1ea8d5 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/kraken_translate_test1.tab @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff --git a/tool_collections/kraken/kraken_translate/test-data/kraken_translate_test1_output.tab b/tool_collections/kraken/kraken_translate/test-data/kraken_translate_test1_output.tab new file mode 100644 index 00000000000..e187cd5469c --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/kraken_translate_test1_output.tab @@ -0,0 +1,4 @@ +gi|145231|gb|M33724.1|ECOALPHOA root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 +gi|145232|gb|M33725.1|ECOALPHOB root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 +gi|145234|gb|M33727.1|ECOALPHOE root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 +gi|146195|gb|J01619.1|ECOGLTA root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 diff --git a/tool_collections/kraken/kraken_translate/test-data/test_database.loc b/tool_collections/kraken/kraken_translate/test-data/test_database.loc new file mode 120000 index 00000000000..03ec4336e45 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/test_database.loc @@ -0,0 +1 @@ +../../test_database.loc \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/test-data/test_db/database.idx b/tool_collections/kraken/kraken_translate/test-data/test_db/database.idx new file mode 120000 index 00000000000..9251273d383 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/test_db/database.idx @@ -0,0 +1 @@ +../../../database.idx \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/test-data/test_db/database.kdb b/tool_collections/kraken/kraken_translate/test-data/test_db/database.kdb new file mode 120000 index 00000000000..64efac5ce08 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/test_db/database.kdb @@ -0,0 +1 @@ +../../../database.kdb \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/test-data/test_db/taxonomy/names.dmp b/tool_collections/kraken/kraken_translate/test-data/test_db/taxonomy/names.dmp new file mode 120000 index 00000000000..f4585471fc2 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/test_db/taxonomy/names.dmp @@ -0,0 +1 @@ +../../../../names.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/test-data/test_db/taxonomy/nodes.dmp b/tool_collections/kraken/kraken_translate/test-data/test_db/taxonomy/nodes.dmp new file mode 120000 index 00000000000..a65d7d41f87 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/test-data/test_db/taxonomy/nodes.dmp @@ -0,0 +1 @@ +../../../../nodes.dmp \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/tool-data/kraken_databases.loc.sample b/tool_collections/kraken/kraken_translate/tool-data/kraken_databases.loc.sample new file mode 120000 index 00000000000..eba8983e9ea --- /dev/null +++ b/tool_collections/kraken/kraken_translate/tool-data/kraken_databases.loc.sample @@ -0,0 +1 @@ +../../kraken_databases.loc.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/tool_data_table_conf.xml.sample b/tool_collections/kraken/kraken_translate/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..332baf440e9 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/kraken/kraken_translate/tool_data_table_conf.xml.test b/tool_collections/kraken/kraken_translate/tool_data_table_conf.xml.test new file mode 120000 index 00000000000..f8050b61701 --- /dev/null +++ b/tool_collections/kraken/kraken_translate/tool_data_table_conf.xml.test @@ -0,0 +1 @@ +../tool_data_table_conf.xml.test \ No newline at end of file diff --git a/tool_collections/kraken/macros.xml b/tool_collections/kraken/macros.xml new file mode 100644 index 00000000000..1a47b71a032 --- /dev/null +++ b/tool_collections/kraken/macros.xml @@ -0,0 +1,27 @@ + + + + + kraken + + + + + + + + + + + + + + + 10.1186/gb-2014-15-3-r46 + + + --db ${kraken_database.fields.name} + export KRAKEN_DB_PATH="${kraken_database.fields.path}" + diff --git a/tool_collections/kraken/names.dmp b/tool_collections/kraken/names.dmp new file mode 100644 index 00000000000..fa5e7ef33d4 --- /dev/null +++ b/tool_collections/kraken/names.dmp @@ -0,0 +1,74 @@ +83333 | Escherichia coli K-12 | | scientific name | +83333 | Escherichia coli K12 | | equivalent name | +562 | "Bacillus coli" Migula 1895 | | authority | +562 | "Bacterium coli commune" Escherich 1885 | | authority | +562 | "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896 | | authority | +562 | ATCC 11775 | | type material | +562 | Bacillus coli | | synonym | +562 | Bacterium coli | | synonym | +562 | Bacterium coli commune | | synonym | +562 | CCUG 24 | | type material | +562 | CCUG 29300 | | type material | +562 | CIP 54.8 | | type material | +562 | DSM 30083 | | type material | +562 | Enterococcus coli | | synonym | +562 | Escherchia coli | | misspelling | +562 | Escherichia coli | | scientific name | +562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | | authority | +562 | Escherichia sp. MAR | | includes | +562 | Escherichia/Shigella coli | | equivalent name | +562 | Eschericia coli | | misspelling | +562 | JCM 1649 | | type material | +562 | LMG 2092 | | type material | +562 | NBRC 102203 | | type material | +562 | NCCB 54008 | | type material | +562 | NCTC 9001 | | type material | +562 | bacterium 10a | | includes | +562 | bacterium E3 | | includes | +561 | Escherchia | | misspelling | +561 | Escherichia | | scientific name | +561 | Escherichia Castellani and Chalmers 1919 | | authority | +543 | Enterobacteraceae | | synonym | +543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae | | scientific name | +543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae Rahn 1937 | | synonym | +543 | gamma-3 proteobacteria | gamma-3 proteobacteria <#1> | in-part | +91347 | 'Enterobacteriales' | | synonym | +91347 | Enterobacteriaceae and related endosymbionts | | synonym | +91347 | Enterobacteriaceae group | | synonym | +91347 | Enterobacteriales | | scientific name | +91347 | enterobacteria | enterobacteria | blast name | +91347 | gamma-3 proteobacteria | gamma-3 proteobacteria <#5> | in-part | +1236 | Gammaproteobacteria | | scientific name | +1236 | Gammaproteobacteria Garrity et al. 2005 | | synonym | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +1236 | g-proteobacteria | gamma proteos | blast name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1224 | Proteobacteria | | scientific name | +1224 | Proteobacteria Garrity et al. 2005 | | authority | +1224 | Proteobacteria [class] Stackebrandt et al. 1988 | | authority | +1224 | not Proteobacteria Cavalier-Smith 2002 | | authority | +1224 | proteobacteria | proteobacteria | blast name | +1224 | purple bacteria | | common name | +1224 | purple bacteria and relatives | | common name | +1224 | purple non-sulfur bacteria | | common name | +1224 | purple photosynthetic bacteria | | common name | +1224 | purple photosynthetic bacteria and relatives | | common name | +2 | Bacteria | Bacteria | scientific name | +2 | Monera | Monera | in-part | +2 | Procaryotae | Procaryotae | in-part | +2 | Prokaryota | Prokaryota | in-part | +2 | Prokaryotae | Prokaryotae | in-part | +2 | bacteria | bacteria | blast name | +2 | eubacteria | | genbank common name | +2 | not Bacteria Haeckel 1894 | | synonym | +2 | prokaryote | prokaryote | in-part | +2 | prokaryotes | prokaryotes | in-part | +1 | all | | synonym | +1 | root | | scientific name | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | diff --git a/tool_collections/kraken/nodes.dmp b/tool_collections/kraken/nodes.dmp new file mode 100644 index 00000000000..4e292c27101 --- /dev/null +++ b/tool_collections/kraken/nodes.dmp @@ -0,0 +1,10 @@ +83333 | 562 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | diff --git a/tool_collections/kraken/test_database.loc b/tool_collections/kraken/test_database.loc new file mode 100644 index 00000000000..8441f152d69 --- /dev/null +++ b/tool_collections/kraken/test_database.loc @@ -0,0 +1 @@ +test_db test_db ${__HERE__} \ No newline at end of file diff --git a/tool_collections/kraken/tool_data_table_conf.xml.sample b/tool_collections/kraken/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..c7763ac28af --- /dev/null +++ b/tool_collections/kraken/tool_data_table_conf.xml.sample @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+ diff --git a/tool_collections/kraken/tool_data_table_conf.xml.test b/tool_collections/kraken/tool_data_table_conf.xml.test new file mode 100644 index 00000000000..690ae6b4748 --- /dev/null +++ b/tool_collections/kraken/tool_data_table_conf.xml.test @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+ diff --git a/tool_collections/samtools/bam_to_cram/.shed.yml b/tool_collections/samtools/bam_to_cram/.shed.yml new file mode 100644 index 00000000000..06dc6400cce --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/.shed.yml @@ -0,0 +1,13 @@ +categories: +- Convert Formats +- SAM +description: Converts alignments in BAM format to CRAM format. +long_description: | + This tool uses the SAMtools toolkit to convert BAM to CRAM files. The CRAM + format does additional compression relative to the reference genome which + makes the compression more efficient in terms of file size. +name: samtools_bam_to_cram +owner: devteam +homepage_url: https://samtools.github.io/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram +type: unrestricted diff --git a/tool_collections/samtools/bam_to_cram/macros.xml b/tool_collections/samtools/bam_to_cram/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/bam_to_cram/samtools_bam_to_cram.xml b/tool_collections/samtools/bam_to_cram/samtools_bam_to_cram.xml new file mode 100644 index 00000000000..0ac0ef7ae79 --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/samtools_bam_to_cram.xml @@ -0,0 +1,125 @@ + + convert BAM alignments to CRAM format + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What this tool does** + +Converts alignments from the BAM format to the CRAM format using the SAMTools_ toolkit. The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + + + + diff --git a/tool_collections/samtools/bam_to_cram/test-data/test.bam b/tool_collections/samtools/bam_to_cram/test-data/test.bam new file mode 100644 index 00000000000..5b8d58a2561 Binary files /dev/null and b/tool_collections/samtools/bam_to_cram/test-data/test.bam differ diff --git a/tool_collections/samtools/bam_to_cram/test-data/test.bed b/tool_collections/samtools/bam_to_cram/test-data/test.bed new file mode 100644 index 00000000000..43dabf1de84 --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/test-data/test.bed @@ -0,0 +1 @@ +CHROMOSOME_I 1 120 diff --git a/tool_collections/samtools/bam_to_cram/test-data/test.cram b/tool_collections/samtools/bam_to_cram/test-data/test.cram new file mode 100644 index 00000000000..58d3ad62eac Binary files /dev/null and b/tool_collections/samtools/bam_to_cram/test-data/test.cram differ diff --git a/tool_collections/samtools/bam_to_cram/test-data/test.fa b/tool_collections/samtools/bam_to_cram/test-data/test.fa new file mode 100644 index 00000000000..da7f291fc38 --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/test-data/test.fa @@ -0,0 +1,3 @@ +>CHROMOSOME_I +gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc +ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct diff --git a/tool_collections/samtools/bam_to_cram/test-data/test.sam b/tool_collections/samtools/bam_to_cram/test-data/test.sam new file mode 100644 index 00000000000..055905b377e --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/test-data/test.sam @@ -0,0 +1,15 @@ +@HD VN:1.4 SO:unsorted +@SQ SN:CHROMOSOME_I LN:100 +@RG ID:UNKNOWN SM:UNKNOWN +@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 +@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 +SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU +SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU +SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA 0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.4251890 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###########@BB=BCBBC?B>B;>B@@ADBBB@DBBBBDCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDBA@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.8289592 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################A?@C9@@BC=AABDD@A@DC@CB=@BA?6@CCAAC@+CCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU diff --git a/tool_collections/samtools/bam_to_sam/.shed.yml b/tool_collections/samtools/bam_to_sam/.shed.yml new file mode 100644 index 00000000000..eb02c933c23 --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +- Convert Formats +description: Converts BAM format to SAM format. +long_description: | + This tool uses the SAMtools toolkit to produce a SAM file from a BAM file. +name: bam_to_sam +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam +type: unrestricted diff --git a/tool_collections/samtools/bam_to_sam/bam_to_sam.xml b/tool_collections/samtools/bam_to_sam/bam_to_sam.xml new file mode 100644 index 00000000000..51ed13092db --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/bam_to_sam.xml @@ -0,0 +1,54 @@ + + convert BAM to SAM + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/samtools/bam_to_sam/macros.xml b/tool_collections/samtools/bam_to_sam/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in1.bam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in1.bam new file mode 100644 index 00000000000..307e0c77d58 Binary files /dev/null and b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in1.bam differ diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in1.sam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in1.sam new file mode 100644 index 00000000000..4a1a6a7d5a6 --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in1.sam @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in2.bam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in2.bam new file mode 100644 index 00000000000..258f1321481 Binary files /dev/null and b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in2.bam differ diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in2.sam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in2.sam new file mode 100644 index 00000000000..b16e2455824 --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_in2.sam @@ -0,0 +1,25 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:rg1 SM:s1 +@RG ID:rg2 SM:s3 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out1.sam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out1.sam new file mode 100644 index 00000000000..4a1a6a7d5a6 --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out1.sam @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out2.sam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out2.sam new file mode 100644 index 00000000000..3f20214182b --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out2.sam @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 diff --git a/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out3.sam b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out3.sam new file mode 100644 index 00000000000..a9629207b09 --- /dev/null +++ b/tool_collections/samtools/bam_to_sam/test-data/bam_to_sam_out3.sam @@ -0,0 +1,8 @@ +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 diff --git a/tool_collections/samtools/cram_to_bam/.shed.yml b/tool_collections/samtools/cram_to_bam/.shed.yml new file mode 100644 index 00000000000..9b6fa0293e3 --- /dev/null +++ b/tool_collections/samtools/cram_to_bam/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Convert Formats +- SAM +description: Converts alignments in CRAM format to BAM format. +long_description: | + This tool uses the SAMtools toolkit to convert CRAM to BAM files. +name: samtools_cram_to_bam +owner: devteam +homepage_url: https://samtools.github.io/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam +type: unrestricted diff --git a/tool_collections/samtools/cram_to_bam/macros.xml b/tool_collections/samtools/cram_to_bam/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/cram_to_bam/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/cram_to_bam/samtools_cram_to_bam.xml b/tool_collections/samtools/cram_to_bam/samtools_cram_to_bam.xml new file mode 100644 index 00000000000..7817b182ab7 --- /dev/null +++ b/tool_collections/samtools/cram_to_bam/samtools_cram_to_bam.xml @@ -0,0 +1,114 @@ + + convert CRAM alignments to BAM format + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What this tool does** + +Converts alignments from the CRAM format to the BAM format using the SAMTools_ toolkit. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + + + + diff --git a/tool_collections/samtools/cram_to_bam/test-data b/tool_collections/samtools/cram_to_bam/test-data new file mode 120000 index 00000000000..f633e7fbd66 --- /dev/null +++ b/tool_collections/samtools/cram_to_bam/test-data @@ -0,0 +1 @@ +../bam_to_cram/test-data \ No newline at end of file diff --git a/tool_collections/samtools/macros.xml b/tool_collections/samtools/macros.xml new file mode 100644 index 00000000000..23c3d1d9e8f --- /dev/null +++ b/tool_collections/samtools/macros.xml @@ -0,0 +1,71 @@ + + + + samtools + + + + + + + + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + + 10.1093/bioinformatics/btp352 + 10.1093/bioinformatics/btr076 + 10.1093/bioinformatics/btr509 + + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + + + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + + + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + + + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + + + + + samtools 2>&1 | grep Version + + + + + + + +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + + + diff --git a/tool_collections/samtools/sam_to_bam/.shed.yml b/tool_collections/samtools/sam_to_bam/.shed.yml new file mode 100644 index 00000000000..bf2c6168d02 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +- Convert Formats +description: Convert SAM format to BAM format. +long_description: | + This tool uses the SAMtools toolkit to produce an indexed BAM file based on a sorted input SAM file. +name: sam_to_bam +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam +type: unrestricted diff --git a/tool_collections/samtools/sam_to_bam/macros.xml b/tool_collections/samtools/sam_to_bam/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/sam_to_bam/sam_to_bam.xml b/tool_collections/samtools/sam_to_bam/sam_to_bam.xml new file mode 100644 index 00000000000..dd8e0a65598 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/sam_to_bam.xml @@ -0,0 +1,100 @@ + + convert SAM to BAM + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/samtools/sam_to_bam/test-data/cached_locally/all_fasta.loc b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/all_fasta.loc new file mode 100644 index 00000000000..525bdb3c42d --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/all_fasta.loc @@ -0,0 +1 @@ +chrM chr_m Horse (Equus caballus): equCab2 chrM ${__HERE__}/chrM.fasta diff --git a/tool_collections/samtools/sam_to_bam/test-data/cached_locally/chr_m.fasta b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/chr_m.fasta new file mode 120000 index 00000000000..d467c4ae9d8 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/chr_m.fasta @@ -0,0 +1 @@ +../chr_m.fasta \ No newline at end of file diff --git a/tool_collections/samtools/sam_to_bam/test-data/cached_locally/chr_m.fasta.fai b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/chr_m.fasta.fai new file mode 120000 index 00000000000..9ec361ce008 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/chr_m.fasta.fai @@ -0,0 +1 @@ +../chr_m.fasta.fai \ No newline at end of file diff --git a/tool_collections/samtools/sam_to_bam/test-data/cached_locally/fasta_indexes.loc b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/fasta_indexes.loc new file mode 100644 index 00000000000..525bdb3c42d --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/cached_locally/fasta_indexes.loc @@ -0,0 +1 @@ +chrM chr_m Horse (Equus caballus): equCab2 chrM ${__HERE__}/chrM.fasta diff --git a/tool_collections/samtools/sam_to_bam/test-data/chr_m.fasta b/tool_collections/samtools/sam_to_bam/test-data/chr_m.fasta new file mode 100644 index 00000000000..0ebaea323f0 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/chr_m.fasta @@ -0,0 +1,335 @@ +>chrM +GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA +GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT +TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT +CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA +AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG +ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG +GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA +ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA +AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA +AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA +TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA +AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT +GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC +CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT +CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA +AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT +TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC +TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT +GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT +CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA +CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG +TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA +TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC +TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG +AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG +ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT +AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC +CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT +ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG +AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA +ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA +AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA +ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG +TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA +ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG +TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA +CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA +TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA +AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT +ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC +AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca +taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt +tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg +cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG +ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT +TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC +CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA +TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG +CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG +TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT +CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT +CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT +AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA +AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg +tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt +caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT +GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT +CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG +GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA +CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT +AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC +CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC +CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA +CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG +TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC +ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC +ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA +ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA +TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA +ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG +GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC +ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA +CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC +TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA +CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT +ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact +acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa +ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT +ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT +CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA +TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA +GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC +CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA +TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA +GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA +ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA +TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA +ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT +AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC +AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA +TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT +ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA +GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT +CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC +CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA +AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC +AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT +CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA +TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA +ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC +CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC +TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT +TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT +TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC +CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC +TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG +AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG +CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA +GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG +AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC +TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC +GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA +CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA +TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC +GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC +TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA +TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC +TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA +AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC +TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT +AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT +TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA +TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT +AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT +TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA +TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT +ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG +AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT +TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA +GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT +CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT +TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC +TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT +CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT +ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA +GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG +AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG +GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA +AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata +tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC +ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG +GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA +AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA +GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC +CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT +ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT +ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC +CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT +TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC +TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA +ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT +AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG +TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA +TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA +CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA +TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT +GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT +AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT +ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC +CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA +ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT +CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC +AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC +AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT +TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA +CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA +GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT +ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA +CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT +AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT +AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC +TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC +GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC +CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC +AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC +ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT +ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG +CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT +TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC +CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC +AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG +TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA +GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT +AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT +TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG +TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT +CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG +AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG +TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA +CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA +AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT +ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA +GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC +TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA +AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA +ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC +CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA +TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT +TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC +ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC +ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA +TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC +TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT +CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC +TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT +GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA +TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG +CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC +TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC +CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT +AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA +TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC +ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT +CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT +CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA +AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG +TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC +TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA +GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT +ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC +TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA +AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT +AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA +TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA +AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA +AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA +ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA +ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA +TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC +GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA +GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT +TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA +AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC +CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA +TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA +CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC +CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT +CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA +TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC +TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC +CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG +TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA +TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC +ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC +TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA +TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT +TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC +TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC +AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA +ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC +CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC +GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT +CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA +TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC +TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA +CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT +TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC +CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT +AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT +ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC +TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG +TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC +TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC +CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA +CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG +CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG +ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC +CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG +CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC +TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC +CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT +CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG +TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA +ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC +CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA +CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT +AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC +AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG +TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC +ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC +CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG +AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA +ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT +GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC +GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA +CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG +AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT +ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA +GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC +AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG +GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC +ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT +ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT +ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC +AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT +CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT +CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC +CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT +CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA +ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA +TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT +AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC +CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC +CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT +CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT +CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC +ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT +ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC +TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC +TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT +CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC +CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG +TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA +GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC +AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC +GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG +CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT +TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA +ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA +CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT +CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA +CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA +GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac +ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct +gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt +gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc +acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac +ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA +CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT +GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT +AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA +GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT +TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC +TTCTTCCCCC diff --git a/tool_collections/samtools/sam_to_bam/test-data/chr_m.fasta.fai b/tool_collections/samtools/sam_to_bam/test-data/chr_m.fasta.fai new file mode 100644 index 00000000000..64c0d2c398a --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/chr_m.fasta.fai @@ -0,0 +1 @@ +chrM 16660 6 50 51 diff --git a/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_in1.sam b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_in1.sam new file mode 100644 index 00000000000..85ba34517bc --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_in1.sam @@ -0,0 +1,13 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chrM LN:100001 +@RG ID:rg1 SM:s1 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 diff --git a/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_noheader_in2.sam b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_noheader_in2.sam new file mode 100644 index 00000000000..87881711adc --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_noheader_in2.sam @@ -0,0 +1,10 @@ +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 diff --git a/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out1.bam b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out1.bam new file mode 100644 index 00000000000..35992dfd291 Binary files /dev/null and b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out1.bam differ diff --git a/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out2.bam b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out2.bam new file mode 100644 index 00000000000..35992dfd291 Binary files /dev/null and b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out2.bam differ diff --git a/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out3.bam b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out3.bam new file mode 100644 index 00000000000..e47f62a31f8 Binary files /dev/null and b/tool_collections/samtools/sam_to_bam/test-data/sam_to_bam_out3.bam differ diff --git a/tool_collections/samtools/sam_to_bam/tool-data/fasta_indexes.loc.sample b/tool_collections/samtools/sam_to_bam/tool-data/fasta_indexes.loc.sample new file mode 100644 index 00000000000..fd8fb70ac28 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/tool-data/fasta_indexes.loc.sample @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff --git a/tool_collections/samtools/sam_to_bam/tool_data_table_conf.xml.sample b/tool_collections/samtools/sam_to_bam/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..c34ade01890 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/tool_data_table_conf.xml.sample @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff --git a/tool_collections/samtools/sam_to_bam/tool_data_table_conf.xml.test b/tool_collections/samtools/sam_to_bam/tool_data_table_conf.xml.test new file mode 100644 index 00000000000..a71a944e38c --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/tool_data_table_conf.xml.test @@ -0,0 +1,10 @@ + + + value, dbkey, name, path + +
+ + value, dbkey, name, path + +
+ \ No newline at end of file diff --git a/tool_collections/samtools/samtools_bedcov/.shed.yml b/tool_collections/samtools/samtools_bedcov/.shed.yml new file mode 100644 index 00000000000..dd880132524 --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +- Sequence Analysis +description: Calculate read depth on BAM files +long_description: | + This tool uses the SAMtools toolkit to produce read depth per BED region. +name: samtools_bedcov +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov +type: unrestricted diff --git a/tool_collections/samtools/samtools_bedcov/macros.xml b/tool_collections/samtools/samtools_bedcov/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_bedcov/samtools_bedcov.xml b/tool_collections/samtools/samtools_bedcov/samtools_bedcov.xml new file mode 100644 index 00000000000..2172e5d2e00 --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/samtools_bedcov.xml @@ -0,0 +1,52 @@ + + calculate read depth for a set of genomic intervals + + macros.xml + + + + + '${output}' + ]]> + + + + + + + + + + + + + + + + + + + + +**What it does** + +Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command:: + + samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT] + + + + + diff --git a/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.1.bed b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.1.bed new file mode 100644 index 00000000000..d25dd55f082 --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.1.bed @@ -0,0 +1,3 @@ +eboVir3 500 1500 +eboVir3 1500 2000 +eboVir3 1500 3000 diff --git a/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.2.bam b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.2.bam new file mode 100644 index 00000000000..2fdd7354b8b Binary files /dev/null and b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.2.bam differ diff --git a/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.2.bed b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.2.bed new file mode 100644 index 00000000000..d25dd55f082 --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.2.bed @@ -0,0 +1,3 @@ +eboVir3 500 1500 +eboVir3 1500 2000 +eboVir3 1500 3000 diff --git a/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.bam b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.bam new file mode 100644 index 00000000000..c0e64957d92 Binary files /dev/null and b/tool_collections/samtools/samtools_bedcov/test-data/eboVir3.bam differ diff --git a/tool_collections/samtools/samtools_bedcov/test-data/samtools_bedcov_out1.tab b/tool_collections/samtools/samtools_bedcov/test-data/samtools_bedcov_out1.tab new file mode 100644 index 00000000000..ce32b596e0b --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/test-data/samtools_bedcov_out1.tab @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 +eboVir3 1500 2000 3009 +eboVir3 1500 3000 9986 diff --git a/tool_collections/samtools/samtools_bedcov/test-data/samtools_bedcov_out2.tab b/tool_collections/samtools/samtools_bedcov/test-data/samtools_bedcov_out2.tab new file mode 100644 index 00000000000..4a12f060dfe --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/test-data/samtools_bedcov_out2.tab @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 2094 +eboVir3 1500 2000 3009 1064 +eboVir3 1500 3000 9986 3455 diff --git a/tool_collections/samtools/samtools_calmd/.shed.yml b/tool_collections/samtools/samtools_calmd/.shed.yml new file mode 100644 index 00000000000..5a33b501fc9 --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/.shed.yml @@ -0,0 +1,10 @@ +categories: +- SAM +description: recalculate MD/NM tags +long_description: | + Generates the MD tag using ``samtools calmd`` command. +name: samtools_calmd +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd +type: unrestricted diff --git a/tool_collections/samtools/samtools_calmd/macros.xml b/tool_collections/samtools/samtools_calmd/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_calmd/samtools_calmd.xml b/tool_collections/samtools/samtools_calmd/samtools_calmd.xml new file mode 100644 index 00000000000..c7eb1450694 --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/samtools_calmd.xml @@ -0,0 +1,103 @@ + + recalculate MD/NM tags + + macros.xml + + + + + "$calmd_output" + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options:: + + -e change identical bases to '=' + -A modify the quality string + -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A) + -E extended BAQ for better sensitivity but lower specificity + +----- + +**NM and MD tags** + +From SAM format specification:: + + MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 + NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping + +See refernces for more information about SAM format tags. + + + + diff --git a/tool_collections/samtools/samtools_calmd/test-data/phiX.bam b/tool_collections/samtools/samtools_calmd/test-data/phiX.bam new file mode 100644 index 00000000000..1375552cf36 Binary files /dev/null and b/tool_collections/samtools/samtools_calmd/test-data/phiX.bam differ diff --git a/tool_collections/samtools/samtools_calmd/test-data/phiX.fasta b/tool_collections/samtools/samtools_calmd/test-data/phiX.fasta new file mode 100644 index 00000000000..53df885dc48 --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/test-data/phiX.fasta @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + diff --git a/tool_collections/samtools/samtools_calmd/test-data/samtools_calmd_out_1.bam b/tool_collections/samtools/samtools_calmd/test-data/samtools_calmd_out_1.bam new file mode 100644 index 00000000000..8a59449a5d1 Binary files /dev/null and b/tool_collections/samtools/samtools_calmd/test-data/samtools_calmd_out_1.bam differ diff --git a/tool_collections/samtools/samtools_calmd/test-data/samtools_calmd_out_2.bam b/tool_collections/samtools/samtools_calmd/test-data/samtools_calmd_out_2.bam new file mode 100644 index 00000000000..90808fd28ed Binary files /dev/null and b/tool_collections/samtools/samtools_calmd/test-data/samtools_calmd_out_2.bam differ diff --git a/tool_collections/samtools/samtools_calmd/tool-data/fasta_indexes.loc.sample b/tool_collections/samtools/samtools_calmd/tool-data/fasta_indexes.loc.sample new file mode 100644 index 00000000000..fd8fb70ac28 --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/tool-data/fasta_indexes.loc.sample @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff --git a/tool_collections/samtools/samtools_calmd/tool_data_table_conf.xml.sample b/tool_collections/samtools/samtools_calmd/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..a1c5e1ad88e --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/tool_data_table_conf.xml.sample @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff --git a/tool_collections/samtools/samtools_flagstat/.shed.yml b/tool_collections/samtools/samtools_flagstat/.shed.yml new file mode 100644 index 00000000000..8b20fb87320 --- /dev/null +++ b/tool_collections/samtools/samtools_flagstat/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +- Statistics +description: Provides simple stats on BAM files. +long_description: | + This tool uses the SAMtools toolkit to produce simple stats on a BAM file. +name: samtools_flagstat +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat +type: unrestricted diff --git a/tool_collections/samtools/samtools_flagstat/macros.xml b/tool_collections/samtools/samtools_flagstat/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_flagstat/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_flagstat/samtools_flagstat.xml b/tool_collections/samtools/samtools_flagstat/samtools_flagstat.xml new file mode 100644 index 00000000000..b78d6feaa43 --- /dev/null +++ b/tool_collections/samtools/samtools_flagstat/samtools_flagstat.xml @@ -0,0 +1,51 @@ + + tabulate descriptive stats for BAM datset + + + macros.xml + + + + + + '$output1' + ]]> + + + + + + + + + + + + + + + + + +**What it does** + +Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: + + 200 + 0 in total (QC-passed reads + QC-failed reads) + 0 + 0 secondary + 0 + 0 supplementary + 0 + 0 duplicates + 25 + 0 mapped (12.50%:nan%) + 200 + 0 paired in sequencing + 100 + 0 read1 + 100 + 0 read2 + 0 + 0 properly paired (0.00%:nan%) + 0 + 0 with itself and mate mapped + 25 + 0 singletons (12.50%:nan%) + 0 + 0 with mate mapped to a different chr + 0 + 0 with mate mapped to a different chr (mapQ>=5) + + + + diff --git a/tool_collections/samtools/samtools_flagstat/test-data/samtools_flagstat_input1.bam b/tool_collections/samtools/samtools_flagstat/test-data/samtools_flagstat_input1.bam new file mode 100644 index 00000000000..665d3e03028 Binary files /dev/null and b/tool_collections/samtools/samtools_flagstat/test-data/samtools_flagstat_input1.bam differ diff --git a/tool_collections/samtools/samtools_flagstat/test-data/samtools_flagstat_out1.txt b/tool_collections/samtools/samtools_flagstat/test-data/samtools_flagstat_out1.txt new file mode 100644 index 00000000000..f423a1614d9 --- /dev/null +++ b/tool_collections/samtools/samtools_flagstat/test-data/samtools_flagstat_out1.txt @@ -0,0 +1,13 @@ +200 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 secondary +0 + 0 supplementary +0 + 0 duplicates +25 + 0 mapped (12.50% : N/A) +200 + 0 paired in sequencing +100 + 0 read1 +100 + 0 read2 +0 + 0 properly paired (0.00% : N/A) +0 + 0 with itself and mate mapped +25 + 0 singletons (12.50% : N/A) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5) diff --git a/tool_collections/samtools/samtools_idxstats/.shed.yml b/tool_collections/samtools/samtools_idxstats/.shed.yml new file mode 100644 index 00000000000..445ef516ffc --- /dev/null +++ b/tool_collections/samtools/samtools_idxstats/.shed.yml @@ -0,0 +1,12 @@ +categories: +- SAM +- Statistics +description: BAM mapping statistics (using samtools idxstats) +long_description: | + Runs "samtools idxstats" to get mapping statistics from a sorted + index BAM file as a tabular output file. +name: samtools_idxstats +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats +type: unrestricted diff --git a/tool_collections/samtools/samtools_idxstats/macros.xml b/tool_collections/samtools/samtools_idxstats/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_idxstats/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml b/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml new file mode 100644 index 00000000000..5297ad61b0f --- /dev/null +++ b/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml @@ -0,0 +1,66 @@ + + reports stats of the BAM index file + + macros.xml + + + + + '${output}' + ]]> + + + + + + + + + + + + + `_ for the samtools idxstats command +]]> + + + diff --git a/tool_collections/samtools/samtools_idxstats/test-data/phiX.bam b/tool_collections/samtools/samtools_idxstats/test-data/phiX.bam new file mode 100644 index 00000000000..e7c52270025 Binary files /dev/null and b/tool_collections/samtools/samtools_idxstats/test-data/phiX.bam differ diff --git a/tool_collections/samtools/samtools_idxstats/test-data/samtools_idxstats_out.tabular b/tool_collections/samtools/samtools_idxstats/test-data/samtools_idxstats_out.tabular new file mode 100644 index 00000000000..f51b037ac21 --- /dev/null +++ b/tool_collections/samtools/samtools_idxstats/test-data/samtools_idxstats_out.tabular @@ -0,0 +1,2 @@ +phiX174 5386 972 18 +* 0 0 10 diff --git a/tool_collections/samtools/samtools_mpileup/.shed.yml b/tool_collections/samtools/samtools_mpileup/.shed.yml new file mode 100644 index 00000000000..513cf55e3d3 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/.shed.yml @@ -0,0 +1,13 @@ +categories: +- SAM +- Variant Analysis +description: MPileup SNP and indel caller +long_description: | + Generate BCF or pileup for one or multiple BAM files. Alignment + records are grouped by sample identifiers in @RG header lines. If sample identifiers + are absent, each input file is regarded as one sample. +name: samtools_mpileup +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup +type: unrestricted diff --git a/tool_collections/samtools/samtools_mpileup/macros.xml b/tool_collections/samtools/samtools_mpileup/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_mpileup/samtools_mpileup.xml b/tool_collections/samtools/samtools_mpileup/samtools_mpileup.xml new file mode 100644 index 00000000000..9d703fd5a8f --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/samtools_mpileup.xml @@ -0,0 +1,386 @@ + + multi-way pileup of variants + + macros.xml + + + + + "$output_log" + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/samtools/samtools_mpileup/test-data/phiX.bam b/tool_collections/samtools/samtools_mpileup/test-data/phiX.bam new file mode 100644 index 00000000000..1375552cf36 Binary files /dev/null and b/tool_collections/samtools/samtools_mpileup/test-data/phiX.bam differ diff --git a/tool_collections/samtools/samtools_mpileup/test-data/phiX.fasta b/tool_collections/samtools/samtools_mpileup/test-data/phiX.fasta new file mode 100644 index 00000000000..53df885dc48 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/phiX.fasta @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + diff --git a/tool_collections/samtools/samtools_mpileup/test-data/phiX_1.bam b/tool_collections/samtools/samtools_mpileup/test-data/phiX_1.bam new file mode 100644 index 00000000000..a1aae19efa4 Binary files /dev/null and b/tool_collections/samtools/samtools_mpileup/test-data/phiX_1.bam differ diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_in_1.bam b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_in_1.bam new file mode 100644 index 00000000000..07a05ba9d4e Binary files /dev/null and b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_in_1.bam differ diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_1.log.txt b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_1.log.txt new file mode 100644 index 00000000000..43ec7ed1b9d --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_1.log.txt @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files + Set max per-file depth to 8000 diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_1.pileup b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_1.pileup new file mode 100644 index 00000000000..fad9cab45f6 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_1.pileup @@ -0,0 +1,43 @@ +phiX174 1411 A 0 +phiX174 1412 G 0 +phiX174 1413 C 0 +phiX174 1414 G 0 +phiX174 1415 C 0 +phiX174 1416 C 0 +phiX174 1417 G 0 +phiX174 1418 T 0 +phiX174 1419 G 0 +phiX174 1420 G 0 +phiX174 1421 A 0 +phiX174 1422 T 0 +phiX174 1423 G 0 +phiX174 1424 C 0 +phiX174 1425 C 0 +phiX174 1426 T 0 +phiX174 1427 G 0 +phiX174 1428 A 0 +phiX174 1429 C 0 +phiX174 1430 C 0 +phiX174 1431 G 0 +phiX174 1432 T 0 +phiX174 1433 A 0 +phiX174 1434 C 0 +phiX174 1435 C 0 +phiX174 1436 G 0 +phiX174 1437 A 0 +phiX174 1438 G 0 +phiX174 1439 G 0 +phiX174 1440 C 0 +phiX174 1441 T 0 +phiX174 1442 A 0 +phiX174 1443 A 0 +phiX174 1444 C 0 +phiX174 1445 C 0 +phiX174 1446 C 0 +phiX174 1447 T 0 +phiX174 1448 A 0 +phiX174 1449 A 0 +phiX174 1450 T 0 +phiX174 1451 G 0 +phiX174 1452 A 0 +phiX174 1453 G 0 diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_2.log.txt b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_2.log.txt new file mode 100644 index 00000000000..43ec7ed1b9d --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_2.log.txt @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files + Set max per-file depth to 8000 diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_2.vcf b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_2.vcf new file mode 100644 index 00000000000..5a1dd7641ba --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_2.vcf @@ -0,0 +1,22 @@ +##fileformat=VCFv4.2 +##FILTER= +##samtoolsVersion=1.1+htslib-1.1 +##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat +##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat +##contig= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_3.pileup b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_3.pileup new file mode 100644 index 00000000000..f494a27538d --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_3.pileup @@ -0,0 +1,43 @@ +phiX174 1411 A 1 ^P. $ P 1 +phiX174 1412 G 3 .^D.^F. "$$ PDF 2,1,1 +phiX174 1413 C 5 ...^D.^F. """$$ PDFDF 3,2,2,1,1 +phiX174 1414 G 6 .....^F. #####$ PDFDFF 4,3,3,2,2,1 +phiX174 1415 C 7 ......^F. %%%%%%& PDFDFFF 5,4,4,3,3,2,1 +phiX174 1416 C 8 .......^F. $$$$$$$$ PDFDFFFF 6,5,5,4,4,3,2,1 +phiX174 1417 G 9 ........^F. "#######$ PDFDFFFFF 7,6,6,5,5,4,3,2,1 +phiX174 1418 T 10 .........^F. """""""""$ PDFDFFFFFF 8,7,7,6,6,5,4,3,2,1 +phiX174 1419 G 10 .......... """""'&'%$ PDFDFFFFFF 9,8,8,7,7,6,5,4,3,2 +phiX174 1420 G 10 .......... """""""""" PDFDFFFFFF 10,9,9,8,8,7,6,5,4,3 +phiX174 1421 A 10 .......... """""""""" PDFDFFFFFF 11,10,10,9,9,8,7,6,5,4 +phiX174 1422 T 10 .......... """""""""" PDFDFFFFFF 12,11,11,10,10,9,8,7,6,5 +phiX174 1423 G 10 .......... """""""""# PDFDFFFFFF 13,12,12,11,11,10,9,8,7,6 +phiX174 1424 C 10 ..A.AAAAAA %""""""""" PDFDFFFFFF 14,13,13,12,12,11,10,9,8,7 +phiX174 1425 C 10 .......... $$$""""""" PDFDFFFFFF 15,14,14,13,13,12,11,10,9,8 +phiX174 1426 T 10 .......... #####""""" PDFDFFFFFF 16,15,15,14,14,13,12,11,10,9 +phiX174 1427 G 10 .......... ######"""" PDFDFFFFFF 17,16,16,15,15,14,13,12,11,10 +phiX174 1428 A 10 .......... """""""""" PDFDFFFFFF 18,17,17,16,16,15,14,13,12,11 +phiX174 1429 C 10 .......... ((((((&("" PDFDFFFFFF 19,18,18,17,17,16,15,14,13,12 +phiX174 1430 C 10 .......... $$$$$$$$$" PDFDFFFFFF 20,19,19,18,18,17,16,15,14,13 +phiX174 1431 G 10 .......... ########## PDFDFFFFFF 21,20,20,19,19,18,17,16,15,14 +phiX174 1432 T 10 .......... """""""""" PDFDFFFFFF 22,21,21,20,20,19,18,17,16,15 +phiX174 1433 A 10 .......... ########## PDFDFFFFFF 23,22,22,21,21,20,19,18,17,16 +phiX174 1434 C 10 .......... ((((((&(%$ PDFDFFFFFF 24,23,23,22,22,21,20,19,18,17 +phiX174 1435 C 10 .......... $$$$$$$$$$ PDFDFFFFFF 25,24,24,23,23,22,21,20,19,18 +phiX174 1436 G 10 .......... ########## PDFDFFFFFF 26,25,25,24,24,23,22,21,20,19 +phiX174 1437 A 10 .......... """""""""! PDFDFFFFFF 27,26,26,25,25,24,23,22,21,20 +phiX174 1438 G 10 .......... """""####! PDFDFFFFFF 28,27,27,26,26,25,24,23,22,21 +phiX174 1439 G 10 .......... """""""""! PDFDFFFFFF 29,28,28,27,27,26,25,24,23,22 +phiX174 1440 C 10 .......... """""""""! PDFDFFFFFF 30,29,29,28,28,27,26,25,24,23 +phiX174 1441 T 10 .......... """"""""#! PDFDFFFFFF 31,30,30,29,29,28,27,26,25,24 +phiX174 1442 A 10 .......... $$$%%%&&%! PDFDFFFFFF 32,31,31,30,30,29,28,27,26,25 +phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! PDFDFFFFFF 33,32,32,31,31,30,29,28,27,26 +phiX174 1444 C 10 **.*...... !!"!"""""! PDFDFFFFFF 34,33,33,32,32,31,30,29,28,27 +phiX174 1445 C 10 .......... !!&!%%%&%! PDFDFFFFFF 34,33,34,32,33,32,31,30,29,28 +phiX174 1446 C 10 .......... !!"!"""""! PDFDFFFFFF 35,34,35,33,34,33,32,31,30,29 +phiX174 1447 T 10 .$..$....... !!#!"""""! PDFDFFFFFF 36,35,36,34,35,34,33,32,31,30 +phiX174 1448 A 8 .$..$..... !!#%%$$! DDFFFFFF 36,35,36,35,34,33,32,31 +phiX174 1449 A 6 .$.$.... !""""! DFFFFF 36,36,35,34,33,32 +phiX174 1450 T 4 .$... """! FFFF 36,35,34,33 +phiX174 1451 G 3 .$.. #"! FFF 36,35,34 +phiX174 1452 A 2 .$. "! FF 36,35 +phiX174 1453 G 1 .$ ! F 36 diff --git a/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_4.vcf b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_4.vcf new file mode 100644 index 00000000000..ddc2d30ad2e --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/test-data/samtools_mpileup_out_4.vcf @@ -0,0 +1,22 @@ +##fileformat=VCFv4.2 +##FILTER= +##samtoolsVersion=1.1+htslib-1.1 +##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa -C 0 -d 200 -E -q 0 -Q 43 -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_756.dat /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat +##reference=file:///var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa +##contig= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat diff --git a/tool_collections/samtools/samtools_mpileup/tool-data/fasta_indexes.loc.sample b/tool_collections/samtools/samtools_mpileup/tool-data/fasta_indexes.loc.sample new file mode 100644 index 00000000000..fd8fb70ac28 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/tool-data/fasta_indexes.loc.sample @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff --git a/tool_collections/samtools/samtools_mpileup/tool_data_table_conf.xml.sample b/tool_collections/samtools/samtools_mpileup/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..c34ade01890 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/tool_data_table_conf.xml.sample @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff --git a/tool_collections/samtools/samtools_phase/.shed.yml b/tool_collections/samtools/samtools_phase/.shed.yml new file mode 100644 index 00000000000..39b64cb878e --- /dev/null +++ b/tool_collections/samtools/samtools_phase/.shed.yml @@ -0,0 +1,9 @@ +categories: +- SAM +- Variant Analysis +description: Call and phase heterozygous SNPs +name: samtools_phase +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase +type: unrestricted diff --git a/tool_collections/samtools/samtools_phase/macros.xml b/tool_collections/samtools/samtools_phase/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_phase/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_phase/samtools_phase.xml b/tool_collections/samtools/samtools_phase/samtools_phase.xml new file mode 100644 index 00000000000..e1037845581 --- /dev/null +++ b/tool_collections/samtools/samtools_phase/samtools_phase.xml @@ -0,0 +1,134 @@ + + heterozygous SNPs + + macros.xml + + + + + '$phase_sets' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Call and phase heterozygous SNPs + +------ + +.. list-table:: **Options** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -k + - INT + - Block length + - 13 + * - -b + - STR + - Prefix of BAM file output + - *null* + * - -q + - INT + - Minimum het phred-LOD + - 37 + * - -Q + - INT + - Min base quality in het calling + - 13 + * - -D + - INT + - Max read depth + - 256 + * - -D + - BOOLEAN + - Do not attempt to fix chimeras + - *off* + * - -A + - BOOLEAN + - Drop reads with ambiguous phase + - *off* + + + + diff --git a/tool_collections/samtools/samtools_phase/test-data/empty_file.bam b/tool_collections/samtools/samtools_phase/test-data/empty_file.bam new file mode 100644 index 00000000000..e69de29bb2d diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_in_1.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_in_1.bam new file mode 100644 index 00000000000..340e7823c56 Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_in_1.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_in_2.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_in_2.bam new file mode 100644 index 00000000000..7c17412c581 Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_in_2.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_log.txt b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_log.txt new file mode 100644 index 00000000000..a2f4cd4a214 --- /dev/null +++ b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_log.txt @@ -0,0 +1,30 @@ +CC +CC Descriptions: +CC +CC CC comments +CC PS start of a phase set +CC FL filtered region +CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered +CC EV supporting reads; SAM format +CC // end of a phase set +CC +CC Formats of PS, FL and M[012] lines (1-based coordinates): +CC +CC PS chr phaseSetStart phaseSetEnd +CC FL chr filterStart filterEnd +CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1 +CC +CC +PS chrI 1187 1290 +M1 chrI 1187 1187 T A 1 2 0 4 0 +M1 chrI 1187 1216 T A 2 3 0 4 0 +M1 chrI 1187 1222 C A 3 3 0 3 1 +M1 chrI 1187 1290 A T 4 1 0 0 0 +EV 0 chrI 1 40 3M * 0 0 AAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1145 +EV 0 chrI 1 40 3M * 0 0 TTC * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1157 +EV 0 chrI 1 40 3M * 0 0 TTC * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1141 +EV 0 chrI 1 40 3M * 0 0 AAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1147 +EV 0 chrI 1 40 3M * 0 0 AAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1176 +EV 0 chrI 1 40 3M * 0 0 AAC * YP:i:1 YF:i:0 YI:i:2 YO:i:1 YS:i:1164 +EV 0 chrI 2 40 3M * 0 0 TCA * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1215 +// diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_phase0.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_phase0.bam new file mode 100644 index 00000000000..14d56ffce89 Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_phase0.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_phase1.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_phase1.bam new file mode 100644 index 00000000000..557a4c50fbd Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_1_phase1.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_log.txt b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_log.txt new file mode 100644 index 00000000000..f307b6c0346 --- /dev/null +++ b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_log.txt @@ -0,0 +1,65 @@ +CC +CC Descriptions: +CC +CC CC comments +CC PS start of a phase set +CC FL filtered region +CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered +CC EV supporting reads; SAM format +CC // end of a phase set +CC +CC Formats of PS, FL and M[012] lines (1-based coordinates): +CC +CC PS chr phaseSetStart phaseSetEnd +CC FL chr filterStart filterEnd +CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1 +CC +CC +PS chrI 1412 1542 +M1 chrI 1412 1412 T C 1 7 0 9 0 +M1 chrI 1412 1414 G A 2 7 0 9 0 +M1 chrI 1412 1421 G A 3 7 0 9 0 +M1 chrI 1412 1471 T C 4 5 0 6 0 +M1 chrI 1412 1542 C T 5 3 0 2 0 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1366 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1343 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1409 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1353 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1358 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1374 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1350 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1379 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1389 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1341 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1340 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1359 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1392 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1407 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1346 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1348 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1444 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1462 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1457 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1468 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1461 +// +PS chrI 3611 3731 +M1 chrI 3611 3611 T A 6 5 0 4 0 +M1 chrI 3611 3659 C T 7 9 0 6 0 +M1 chrI 3611 3731 T A 8 4 0 1 1 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3576 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3571 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3568 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3578 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3590 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3559 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3609 +EV 0 chrI 7 40 2M * 0 0 TA * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3651 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3637 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3647 +EV 0 chrI 7 40 2M * 0 0 TT * YP:i:1 YF:i:0 YI:i:1 YO:i:1 YS:i:3657 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +// diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_phase0.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_phase0.bam new file mode 100644 index 00000000000..1f1aa1a17f2 Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_phase0.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_phase1.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_phase1.bam new file mode 100644 index 00000000000..cf3d2b8ca6a Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_2_phase1.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_log.txt b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_log.txt new file mode 100644 index 00000000000..f307b6c0346 --- /dev/null +++ b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_log.txt @@ -0,0 +1,65 @@ +CC +CC Descriptions: +CC +CC CC comments +CC PS start of a phase set +CC FL filtered region +CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered +CC EV supporting reads; SAM format +CC // end of a phase set +CC +CC Formats of PS, FL and M[012] lines (1-based coordinates): +CC +CC PS chr phaseSetStart phaseSetEnd +CC FL chr filterStart filterEnd +CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1 +CC +CC +PS chrI 1412 1542 +M1 chrI 1412 1412 T C 1 7 0 9 0 +M1 chrI 1412 1414 G A 2 7 0 9 0 +M1 chrI 1412 1421 G A 3 7 0 9 0 +M1 chrI 1412 1471 T C 4 5 0 6 0 +M1 chrI 1412 1542 C T 5 3 0 2 0 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1366 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1343 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1409 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1353 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1358 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1374 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1350 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1379 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1389 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1341 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1340 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1359 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1392 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1407 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1346 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1348 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1444 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1462 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1457 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1468 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1461 +// +PS chrI 3611 3731 +M1 chrI 3611 3611 T A 6 5 0 4 0 +M1 chrI 3611 3659 C T 7 9 0 6 0 +M1 chrI 3611 3731 T A 8 4 0 1 1 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3576 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3571 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3568 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3578 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3590 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3559 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3609 +EV 0 chrI 7 40 2M * 0 0 TA * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3651 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3637 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3647 +EV 0 chrI 7 40 2M * 0 0 TT * YP:i:1 YF:i:0 YI:i:1 YO:i:1 YS:i:3657 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +// diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_phase0.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_phase0.bam new file mode 100644 index 00000000000..1f1aa1a17f2 Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_phase0.bam differ diff --git a/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_phase1.bam b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_phase1.bam new file mode 100644 index 00000000000..17482dd8864 Binary files /dev/null and b/tool_collections/samtools/samtools_phase/test-data/samtools_phase_out_3_phase1.bam differ diff --git a/tool_collections/samtools/samtools_reheader/.shed.yml b/tool_collections/samtools/samtools_reheader/.shed.yml new file mode 100644 index 00000000000..3ca0be0fea6 --- /dev/null +++ b/tool_collections/samtools/samtools_reheader/.shed.yml @@ -0,0 +1,10 @@ +categories: +- SAM +description: Replace SAM header. +long_description: | + Add or replace the header in a SAM or BAM file with a new header. +name: samtools_reheader +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader +type: unrestricted diff --git a/tool_collections/samtools/samtools_reheader/macros.xml b/tool_collections/samtools/samtools_reheader/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_reheader/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_reheader/samtools_reheader.xml b/tool_collections/samtools/samtools_reheader/samtools_reheader.xml new file mode 100644 index 00000000000..31d5fafb203 --- /dev/null +++ b/tool_collections/samtools/samtools_reheader/samtools_reheader.xml @@ -0,0 +1,37 @@ + + copy SAM/BAM header between datasets + + macros.xml + + + + + '${output}' + ]]> + + + + + + + + + + + + + + + +**What it does** + +Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command. + + + + + diff --git a/tool_collections/samtools/samtools_reheader/test-data/reheader_input_file.bam b/tool_collections/samtools/samtools_reheader/test-data/reheader_input_file.bam new file mode 100644 index 00000000000..28b94454aeb Binary files /dev/null and b/tool_collections/samtools/samtools_reheader/test-data/reheader_input_file.bam differ diff --git a/tool_collections/samtools/samtools_reheader/test-data/reheader_input_header.bam b/tool_collections/samtools/samtools_reheader/test-data/reheader_input_header.bam new file mode 100644 index 00000000000..5522416c11a Binary files /dev/null and b/tool_collections/samtools/samtools_reheader/test-data/reheader_input_header.bam differ diff --git a/tool_collections/samtools/samtools_reheader/test-data/reheader_out.bam b/tool_collections/samtools/samtools_reheader/test-data/reheader_out.bam new file mode 100644 index 00000000000..281cbaf2468 Binary files /dev/null and b/tool_collections/samtools/samtools_reheader/test-data/reheader_out.bam differ diff --git a/tool_collections/samtools/samtools_rmdup/.shed.yml b/tool_collections/samtools/samtools_rmdup/.shed.yml new file mode 100644 index 00000000000..f8fd401af27 --- /dev/null +++ b/tool_collections/samtools/samtools_rmdup/.shed.yml @@ -0,0 +1,14 @@ +categories: +- SAM +description: Remove PCR duplicates +long_description: | + This tool uses the SAMtools toolkit to remove potential PCR duplicates: + if multiple read pairs have identical external coordinates, only retain the pair + with highest mapping quality. In the paired-end mode, this command ONLY works with + FR orientation and requires ISIZE is correctly set. It does not work for unpaired + reads (e.g. two ends mapped to different chromosomes or orphan reads). +name: samtools_rmdup +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup +type: unrestricted diff --git a/tool_collections/samtools/samtools_rmdup/macros.xml b/tool_collections/samtools/samtools_rmdup/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_rmdup/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_rmdup/samtools_rmdup.xml b/tool_collections/samtools/samtools_rmdup/samtools_rmdup.xml new file mode 100644 index 00000000000..744fc0f3b41 --- /dev/null +++ b/tool_collections/samtools/samtools_rmdup/samtools_rmdup.xml @@ -0,0 +1,61 @@ + + remove PCR duplicates + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). This tool has the following parameters:: + + -s rmdup for SE reads + -S treat PE reads as SE in rmdup (force -s) + + + + diff --git a/tool_collections/samtools/samtools_rmdup/test-data/samtools-rmdup-input1.bam b/tool_collections/samtools/samtools_rmdup/test-data/samtools-rmdup-input1.bam new file mode 100644 index 00000000000..665d3e03028 Binary files /dev/null and b/tool_collections/samtools/samtools_rmdup/test-data/samtools-rmdup-input1.bam differ diff --git a/tool_collections/samtools/samtools_rmdup/test-data/samtools-rmdup-test1.bam b/tool_collections/samtools/samtools_rmdup/test-data/samtools-rmdup-test1.bam new file mode 100644 index 00000000000..665d3e03028 Binary files /dev/null and b/tool_collections/samtools/samtools_rmdup/test-data/samtools-rmdup-test1.bam differ diff --git a/tool_collections/samtools/samtools_slice_bam/.shed.yml b/tool_collections/samtools/samtools_slice_bam/.shed.yml new file mode 100644 index 00000000000..c305a5b2852 --- /dev/null +++ b/tool_collections/samtools/samtools_slice_bam/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +description: Slice BAM by provided regions +long_description: | + Accepts an input BAM file and an input BED file and creates an + output BAM file containing only those alignments that overlap the provided BED intervals. +name: samtools_slice_bam +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam +type: unrestricted diff --git a/tool_collections/samtools/samtools_slice_bam/macros.xml b/tool_collections/samtools/samtools_slice_bam/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_slice_bam/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml b/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml new file mode 100644 index 00000000000..e9292c4215b --- /dev/null +++ b/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml @@ -0,0 +1,127 @@ + + BAM by genomic regions + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + UCSC Main**. + +This tool is based on ``samtools view`` command. + +@no-chrom-options@ + +]]> + + + diff --git a/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-input.bam b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-input.bam new file mode 100644 index 00000000000..665d3e03028 Binary files /dev/null and b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-input.bam differ diff --git a/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test1.bam b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test1.bam new file mode 100644 index 00000000000..5a03df06af7 Binary files /dev/null and b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test1.bam differ diff --git a/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test2.bam b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test2.bam new file mode 100644 index 00000000000..76c40714b4c Binary files /dev/null and b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test2.bam differ diff --git a/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test3.bam b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test3.bam new file mode 100644 index 00000000000..76c40714b4c Binary files /dev/null and b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice-test3.bam differ diff --git a/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice.bed b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice.bed new file mode 100644 index 00000000000..3dc32e5ce49 --- /dev/null +++ b/tool_collections/samtools/samtools_slice_bam/test-data/bam-slice.bed @@ -0,0 +1,38 @@ +chrM 5 1000 myInterval 0 + +chrM 577 647 TRNF 0 + +chrM 648 1601 RNR1 0 + +chrM 1602 1670 TRNV 0 + +chrM 1671 3229 RNR2 0 + +chrM 3230 3304 TRNL1 0 + +chrM 3307 4262 ND1 0 + +chrM 4263 4331 TRNI 0 + +chrM 4329 4400 TRNQ 0 - +chrM 4402 4469 TRNM 0 + +chrM 4470 5511 ND2 0 + +chrM 5512 5579 TRNW 0 + +chrM 5587 5655 TRNA 0 - +chrM 5657 5729 TRNN 0 - +chrM 5761 5826 TRNC 0 - +chrM 5826 5891 TRNY 0 - +chrM 5904 7445 COX1 0 + +chrM 7446 7514 TRNS1 0 - +chrM 7518 7585 TRND 0 + +chrM 7586 8269 COX2 0 + +chrM 8295 8364 TRNK 0 + +chrM 8366 8572 ATP8 0 + +chrM 8527 9207 ATP6 0 + +chrM 9207 9990 COX3 0 + +chrM 9991 10058 TRNG 0 + +chrM 10059 10404 ND3 0 + +chrM 10405 10469 TRNR 0 + +chrM 10470 10766 ND4L 0 + +chrM 10760 12137 ND4 0 + +chrM 12138 12206 TRNH 0 + +chrM 12207 12265 TRNS2 0 + +chrM 12266 12336 TRNL2 0 + +chrM 12337 14148 ND5 0 + +chrM 14149 14673 ND6 0 - +chrM 14674 14742 TRNE 0 - +chrM 14747 15887 CYTB 0 + +chrM 15888 15953 TRNT 0 + +chrM 15956 16023 TRNP 0 - diff --git a/tool_collections/samtools/samtools_sort/.shed.yml b/tool_collections/samtools/samtools_sort/.shed.yml new file mode 100644 index 00000000000..db06ec5bcec --- /dev/null +++ b/tool_collections/samtools/samtools_sort/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +description: Sort alignments by leftmost coordinates or read name. +long_description: | + This tool uses the SAMtools toolkit to sort alignments by leftmost + coordinates or read names. +name: samtools_sort +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort +type: unrestricted diff --git a/tool_collections/samtools/samtools_sort/macros.xml b/tool_collections/samtools/samtools_sort/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_sort/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_sort/samtools_sort.xml b/tool_collections/samtools/samtools_sort/samtools_sort.xml new file mode 100644 index 00000000000..48f744af243 --- /dev/null +++ b/tool_collections/samtools/samtools_sort/samtools_sort.xml @@ -0,0 +1,46 @@ + + order of storing aligned sequences + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. + + + diff --git a/tool_collections/samtools/samtools_sort/test-data/1.bam b/tool_collections/samtools/samtools_sort/test-data/1.bam new file mode 100644 index 00000000000..95c65de8572 Binary files /dev/null and b/tool_collections/samtools/samtools_sort/test-data/1.bam differ diff --git a/tool_collections/samtools/samtools_sort/test-data/1_sort.bam b/tool_collections/samtools/samtools_sort/test-data/1_sort.bam new file mode 100644 index 00000000000..00ad79a950e Binary files /dev/null and b/tool_collections/samtools/samtools_sort/test-data/1_sort.bam differ diff --git a/tool_collections/samtools/samtools_sort/test-data/1_sort_read_names.bam b/tool_collections/samtools/samtools_sort/test-data/1_sort_read_names.bam new file mode 100644 index 00000000000..bf1c5bc5671 Binary files /dev/null and b/tool_collections/samtools/samtools_sort/test-data/1_sort_read_names.bam differ diff --git a/tool_collections/samtools/samtools_split/.shed.yml b/tool_collections/samtools/samtools_split/.shed.yml new file mode 100644 index 00000000000..3dcb599b5ef --- /dev/null +++ b/tool_collections/samtools/samtools_split/.shed.yml @@ -0,0 +1,11 @@ +categories: +- SAM +description: 'Split a BAM file by read group' +long_description: | + This tool runs the samtools split command in the SAMtools toolkit + to split BAM files by read group. +name: samtools_split +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split +type: unrestricted diff --git a/tool_collections/samtools/samtools_split/macros.xml b/tool_collections/samtools/samtools_split/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_split/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_split/samtools_split.xml b/tool_collections/samtools/samtools_split/samtools_split.xml new file mode 100644 index 00000000000..6d23f4f781f --- /dev/null +++ b/tool_collections/samtools/samtools_split/samtools_split.xml @@ -0,0 +1,47 @@ + + BAM dataset on readgroups + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/samtools/samtools_split/test-data/phiX.bam b/tool_collections/samtools/samtools_split/test-data/phiX.bam new file mode 100644 index 00000000000..093f6b1eab0 Binary files /dev/null and b/tool_collections/samtools/samtools_split/test-data/phiX.bam differ diff --git a/tool_collections/samtools/samtools_split/test-data/phiX_Elephant.bam b/tool_collections/samtools/samtools_split/test-data/phiX_Elephant.bam new file mode 100644 index 00000000000..bc78c469717 Binary files /dev/null and b/tool_collections/samtools/samtools_split/test-data/phiX_Elephant.bam differ diff --git a/tool_collections/samtools/samtools_split/test-data/phiX_Human.bam b/tool_collections/samtools/samtools_split/test-data/phiX_Human.bam new file mode 100644 index 00000000000..7be16ddbb6e Binary files /dev/null and b/tool_collections/samtools/samtools_split/test-data/phiX_Human.bam differ diff --git a/tool_collections/samtools/samtools_split/test-data/phiX_Mouse.bam b/tool_collections/samtools/samtools_split/test-data/phiX_Mouse.bam new file mode 100644 index 00000000000..193d335a414 Binary files /dev/null and b/tool_collections/samtools/samtools_split/test-data/phiX_Mouse.bam differ diff --git a/tool_collections/samtools/samtools_split/test-data/samtools_split_out.bam b/tool_collections/samtools/samtools_split/test-data/samtools_split_out.bam new file mode 100644 index 00000000000..ab39bc05a63 Binary files /dev/null and b/tool_collections/samtools/samtools_split/test-data/samtools_split_out.bam differ diff --git a/tool_collections/samtools/samtools_stats/.shed.yml b/tool_collections/samtools/samtools_stats/.shed.yml new file mode 100644 index 00000000000..2e71c973eb1 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/.shed.yml @@ -0,0 +1,12 @@ +categories: +- SAM +- Statistics +description: Generate statistics for a BAM or SAM file +long_description: | + This tool runs the samtools stats command in the SAMtools toolkit, + collecting statistics from BAM files. The output can be visualized using plot-bamstats. +name: samtools_stats +owner: devteam +homepage_url: http://www.htslib.org/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats +type: unrestricted diff --git a/tool_collections/samtools/samtools_stats/macros.xml b/tool_collections/samtools/samtools_stats/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/samtools/samtools_stats/samtools_stats.xml b/tool_collections/samtools/samtools_stats/samtools_stats.xml new file mode 100644 index 00000000000..c6e330ed404 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/samtools_stats.xml @@ -0,0 +1,301 @@ + + generate statistics for BAM dataset + + macros.xml + + + + + "${output}" + + #if $split_output.split_output_selector == "yes": + #set outputs_to_split = str($split_output.generate_tables).split(',') + && mkdir split && + echo ${split_output.generate_tables} && + + #if 'sn' in $outputs_to_split: + echo "# Summary Numbers" > "split/Summary numbers.tab" && + echo "" >> "split/Summary numbers.tab" && + grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi && + #end if + + #if 'ffq' in $outputs_to_split: + echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" && + grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi && + #end if + + #if 'lfq' in $outputs_to_split: + echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" && + grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi && + #end if + + #if 'mpc' in $outputs_to_split: + echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" && + grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi && + #end if + + #if 'gcf' in $outputs_to_split: + echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" && + grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi && + #end if + + #if 'gcl' in $outputs_to_split: + echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" && + grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi && + #end if + + #if 'gcc' in $outputs_to_split: + echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" && + grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi && + #end if + + #if 'is' in $outputs_to_split: + echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" && + grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- >> "split/Insert sizes.tab" ; fi && + #end if + + #if 'rl' in $outputs_to_split: + echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" && + grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- >> "split/Read lengths.tab" ; fi && + #end if + + #if 'id' in $outputs_to_split: + echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" && + grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- >> "split/Indel distribution.tab" ; fi && + #end if + + #if 'ic' in $outputs_to_split: + echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" && + grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- >> "split/Indels per cycle.tab" ; fi && + #end if + + #if 'cov' in $outputs_to_split: + echo "# Coverage distribution" > "split/Coverage distribution.tab" && + grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi && + #end if + + #if 'gcd' in $outputs_to_split: + echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" && + grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi && + #end if + + ## Unix true command below + + true + + #end if + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ,, Coverage distribution min,max,step [1,1000,1] + -d, --remove-dups Exclude from statistics reads marked as duplicates + -f, --required-flag Required flag, 0 for unset. See also `samtools flags` [0] + -F, --filtering-flag Filtering flag, 0 for unset. See also `samtools flags` [0] + --GC-depth the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4] + -h, --help This help message + -i, --insert-size Maximum insert size [8000] + -I, --id Include only listed read group or sample name + -l, --read-length Include in the statistics only reads with the given read length [] + -m, --most-inserts Report only the main part of inserts [0.99] + -q, --trim-quality The BWA trimming parameter [0] + -r, --ref-seq Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy + will provide options for selecting a reference cached as this Galaxy instance or choosing + one from history. + ]]> + + + diff --git a/tool_collections/samtools/samtools_stats/test-data/phiX.bam b/tool_collections/samtools/samtools_stats/test-data/phiX.bam new file mode 100644 index 00000000000..e7c52270025 Binary files /dev/null and b/tool_collections/samtools/samtools_stats/test-data/phiX.bam differ diff --git a/tool_collections/samtools/samtools_stats/test-data/samtools_stats_input.bam b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_input.bam new file mode 100644 index 00000000000..665d3e03028 Binary files /dev/null and b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_input.bam differ diff --git a/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out1.tab b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out1.tab new file mode 100644 index 00000000000..059c9f042d0 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out1.tab @@ -0,0 +1,1138 @@ +# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_2.dat /tmp/tmpO1aTrb/files/000/dataset_1.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1bd20fd8 58ad2167 29883386 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. 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quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] +GCC 1 21.94 30.10 34.18 13.78 2.04 0.00 +GCC 2 30.00 16.00 11.00 43.00 0.00 0.00 +GCC 3 33.00 25.00 9.00 33.00 0.00 0.00 +GCC 4 17.00 29.00 13.00 41.00 0.00 0.00 +GCC 5 37.00 22.00 12.00 29.00 0.00 0.00 +GCC 6 36.00 26.00 17.00 21.00 0.00 0.00 +GCC 7 29.50 13.50 31.50 25.50 0.00 0.00 +GCC 8 50.50 14.50 19.50 15.50 0.00 0.00 +GCC 9 17.00 33.00 18.00 32.00 0.00 0.00 +GCC 10 37.00 14.00 21.00 28.00 0.00 0.00 +GCC 11 20.50 14.50 29.50 35.50 0.00 0.00 +GCC 12 30.00 24.00 22.00 24.00 0.00 0.00 +GCC 13 27.00 15.00 21.00 37.00 0.00 0.00 +GCC 14 24.24 22.22 26.26 27.27 1.01 0.00 +GCC 15 25.50 20.50 24.50 29.50 0.00 0.00 +GCC 16 31.00 15.00 20.00 34.00 0.00 0.00 +GCC 17 28.00 25.00 14.00 33.00 0.00 0.00 +GCC 18 30.50 28.50 19.50 21.50 0.00 0.00 +GCC 19 29.00 26.00 21.00 24.00 0.00 0.00 +GCC 20 22.50 23.50 17.50 36.50 0.00 0.00 +GCC 21 35.50 17.50 19.50 27.50 0.00 0.00 +GCC 22 37.50 28.50 15.50 18.50 0.00 0.00 +GCC 23 31.31 19.19 13.13 36.36 1.01 0.00 +GCC 24 37.00 12.00 22.00 29.00 0.00 0.00 +GCC 25 35.50 22.50 17.50 24.50 0.00 0.00 +GCC 26 33.50 18.50 15.50 32.50 0.00 0.00 +GCC 27 34.50 14.50 25.50 25.50 0.00 0.00 +GCC 28 31.00 14.00 24.00 31.00 0.00 0.00 +GCC 29 30.00 27.00 24.00 19.00 0.00 0.00 +GCC 30 31.00 20.00 14.00 35.00 0.00 0.00 +GCC 31 33.50 29.50 13.50 23.50 0.00 0.00 +GCC 32 42.50 20.50 19.50 17.50 0.00 0.00 +GCC 33 25.50 23.50 14.50 36.50 0.00 0.00 +GCC 34 39.50 16.50 20.50 23.50 0.00 0.00 +GCC 35 32.50 23.50 21.50 22.50 0.00 0.00 +GCC 36 42.00 25.00 16.00 17.00 0.00 0.00 +GCC 37 38.00 17.00 19.00 26.00 0.00 0.00 +GCC 38 24.00 26.00 25.00 25.00 0.00 0.00 +GCC 39 22.50 41.50 18.50 17.50 0.00 0.00 +GCC 40 32.00 16.00 21.00 31.00 0.00 0.00 +GCC 41 33.00 28.00 19.00 20.00 0.00 0.00 +GCC 42 30.50 25.50 19.50 24.50 0.00 0.00 +GCC 43 35.00 29.00 15.00 21.00 0.00 0.00 +GCC 44 20.00 27.00 22.00 31.00 0.00 0.00 +GCC 45 40.50 21.50 21.50 16.50 0.00 0.00 +GCC 46 26.50 20.50 22.50 30.50 0.00 0.00 +GCC 47 38.50 29.50 16.50 15.50 0.00 0.00 +GCC 48 27.50 24.50 17.50 30.50 0.00 0.00 +GCC 49 28.50 32.50 10.50 28.50 0.00 0.00 +GCC 50 46.50 20.50 9.50 23.50 0.00 0.00 +GCC 51 34.50 28.50 13.50 23.50 0.00 0.00 +GCC 52 41.50 23.50 20.50 14.50 0.00 0.00 +GCC 53 20.00 28.00 26.00 26.00 0.00 0.00 +GCC 54 31.50 18.50 24.50 25.50 0.00 0.00 +GCC 55 30.50 22.50 16.50 30.50 0.00 0.00 +GCC 56 33.50 22.50 13.50 30.50 0.00 0.00 +GCC 57 23.00 24.00 23.00 30.00 0.00 0.00 +GCC 58 25.00 37.00 19.00 19.00 0.00 0.00 +GCC 59 34.00 23.00 24.00 19.00 0.00 0.00 +GCC 60 29.00 28.00 17.00 26.00 0.00 0.00 +GCC 61 25.50 23.50 24.50 26.50 0.00 0.00 +GCC 62 31.50 22.50 16.50 29.50 0.00 0.00 +GCC 63 27.50 28.50 25.50 18.50 0.00 0.00 +GCC 64 33.50 21.50 25.50 19.50 0.00 0.00 +GCC 65 35.50 19.50 18.50 26.50 0.00 0.00 +GCC 66 34.00 25.00 15.00 26.00 0.00 0.00 +GCC 67 37.00 23.00 19.00 21.00 0.00 0.00 +GCC 68 36.50 29.50 13.50 20.50 0.00 0.00 +GCC 69 38.50 19.50 20.50 21.50 0.00 0.00 +GCC 70 38.50 16.50 18.50 26.50 0.00 0.00 +GCC 71 25.50 38.50 21.50 14.50 0.00 0.00 +GCC 72 29.00 29.00 25.00 17.00 0.00 0.00 +GCC 73 32.50 20.50 21.50 25.50 0.00 0.00 +GCC 74 28.50 32.50 12.50 26.50 0.00 0.00 +GCC 75 41.50 12.50 18.50 27.50 0.00 0.00 +GCC 76 24.50 29.50 23.50 22.50 0.00 0.00 +GCC 77 36.00 21.00 18.00 25.00 0.00 0.00 +GCC 78 27.00 34.00 22.00 17.00 0.00 0.00 +GCC 79 21.50 26.50 25.50 26.50 0.00 0.00 +GCC 80 34.00 19.00 28.00 19.00 0.00 0.00 +GCC 81 17.00 26.00 26.00 31.00 0.00 0.00 +GCC 82 31.00 30.00 23.00 16.00 0.00 0.00 +GCC 83 31.50 26.50 12.50 29.50 0.00 0.00 +GCC 84 19.00 41.00 21.00 19.00 0.00 0.00 +GCC 85 37.50 24.50 16.50 21.50 0.00 0.00 +GCC 86 15.00 48.00 15.00 22.00 0.00 0.00 +GCC 87 41.00 16.00 18.00 25.00 0.00 0.00 +GCC 88 23.50 27.50 27.50 21.50 0.00 0.00 +GCC 89 26.50 27.50 26.50 19.50 0.00 0.00 +GCC 90 18.50 23.50 24.50 33.50 0.00 0.00 +GCC 91 27.00 32.00 22.00 19.00 0.00 0.00 +GCC 92 23.50 17.50 27.50 31.50 0.00 0.00 +GCC 93 25.50 37.50 15.50 21.50 0.00 0.00 +GCC 94 27.00 17.00 24.00 32.00 0.00 0.00 +GCC 95 26.77 37.88 14.65 20.71 1.01 0.00 +GCC 96 29.50 25.50 16.50 28.50 0.00 0.00 +GCC 97 29.00 31.00 21.00 19.00 0.00 0.00 +GCC 98 18.18 33.33 22.22 26.26 1.01 0.00 +GCC 99 24.50 33.50 24.50 17.50 0.00 0.00 +GCC 100 24.50 16.50 24.50 34.50 0.00 0.00 +GCC 101 25.00 40.00 19.00 16.00 0.00 0.00 +GCC 102 17.50 17.50 32.50 32.50 0.00 0.00 +GCC 103 31.00 26.00 16.00 27.00 0.00 0.00 +GCC 104 26.50 29.50 20.50 23.50 0.00 0.00 +GCC 105 34.00 33.00 21.00 12.00 0.00 0.00 +GCC 106 23.00 31.00 26.00 20.00 0.00 0.00 +GCC 107 17.68 35.86 23.74 22.73 1.01 0.00 +GCC 108 24.75 30.81 23.74 20.71 1.01 0.00 +GCC 109 17.00 31.00 22.00 30.00 0.00 0.00 +GCC 110 16.16 35.35 24.24 24.24 1.01 0.00 +GCC 111 24.24 32.32 23.23 20.20 1.01 0.00 +GCC 112 37.37 28.28 16.16 18.18 1.01 0.00 +GCC 113 19.70 22.73 32.83 24.75 1.01 0.00 +GCC 114 17.00 31.00 35.00 17.00 0.00 0.00 +GCC 115 29.50 24.50 23.50 22.50 0.00 0.00 +GCC 116 22.00 30.00 34.00 14.00 0.00 0.00 +GCC 117 27.00 23.00 19.00 31.00 0.00 0.00 +GCC 118 25.50 14.50 34.50 25.50 0.00 0.00 +GCC 119 22.50 34.50 20.50 22.50 0.00 0.00 +GCC 120 17.50 24.50 26.50 31.50 0.00 0.00 +GCC 121 27.78 33.84 22.73 15.66 1.01 0.00 +GCC 122 17.00 23.00 25.00 35.00 0.00 0.00 +GCC 123 23.50 46.50 11.50 18.50 0.00 0.00 +GCC 124 9.00 32.00 34.00 25.00 0.00 0.00 +GCC 125 24.00 27.00 19.00 30.00 0.00 0.00 +GCC 126 26.00 17.00 28.00 29.00 0.00 0.00 +GCC 127 26.50 16.50 21.50 35.50 0.00 0.00 +GCC 128 18.00 34.00 31.00 17.00 0.00 0.00 +GCC 129 25.50 25.50 27.50 21.50 0.00 0.00 +GCC 130 25.00 20.00 22.00 33.00 0.00 0.00 +GCC 131 17.50 39.50 24.50 18.50 0.00 0.00 +GCC 132 21.00 28.00 23.00 28.00 0.00 0.00 +GCC 133 13.50 31.50 35.50 19.50 0.00 0.00 +GCC 134 24.50 19.50 30.50 25.50 0.00 0.00 +GCC 135 16.50 23.50 30.50 29.50 0.00 0.00 +GCC 136 28.00 32.00 15.00 25.00 0.00 0.00 +GCC 137 22.50 21.50 30.50 25.50 0.00 0.00 +GCC 138 14.50 34.50 24.50 26.50 0.00 0.00 +GCC 139 20.50 29.50 24.50 25.50 0.00 0.00 +GCC 140 17.00 23.00 30.00 30.00 0.00 0.00 +GCC 141 20.50 23.50 25.50 30.50 0.00 0.00 +GCC 142 18.00 29.00 38.00 15.00 0.00 0.00 +GCC 143 22.00 24.00 27.00 27.00 0.00 0.00 +GCC 144 21.50 30.50 26.50 21.50 0.00 0.00 +GCC 145 22.00 21.00 29.00 28.00 0.00 0.00 +GCC 146 25.00 16.00 39.00 20.00 0.00 0.00 +GCC 147 26.50 22.50 30.50 20.50 0.00 0.00 +GCC 148 12.50 28.50 36.50 22.50 0.00 0.00 +GCC 149 26.50 23.50 23.50 26.50 0.00 0.00 +GCC 150 14.00 29.00 24.00 33.00 0.00 0.00 +GCC 151 19.50 30.50 32.50 17.50 0.00 0.00 +GCC 152 18.50 17.50 29.50 34.50 0.00 0.00 +GCC 153 22.50 22.50 31.50 23.50 0.00 0.00 +GCC 154 22.00 21.00 29.00 28.00 0.00 0.00 +GCC 155 21.00 26.00 19.00 34.00 0.00 0.00 +GCC 156 14.50 23.50 35.50 26.50 0.00 0.00 +GCC 157 22.00 31.00 23.00 24.00 0.00 0.00 +GCC 158 22.50 29.50 24.50 23.50 0.00 0.00 +GCC 159 17.50 12.50 46.50 23.50 0.00 0.00 +GCC 160 24.50 26.50 26.50 22.50 0.00 0.00 +GCC 161 13.00 23.00 45.00 19.00 0.00 0.00 +GCC 162 31.50 16.50 22.50 29.50 0.00 0.00 +GCC 163 19.50 21.50 35.50 23.50 0.00 0.00 +GCC 164 29.00 18.00 21.00 32.00 0.00 0.00 +GCC 165 14.50 17.50 35.50 32.50 0.00 0.00 +GCC 166 17.50 37.50 28.50 16.50 0.00 0.00 +GCC 167 16.50 21.50 31.50 30.50 0.00 0.00 +GCC 168 14.00 25.00 30.00 31.00 0.00 0.00 +GCC 169 18.50 20.50 23.50 37.50 0.00 0.00 +GCC 170 19.00 23.00 28.00 30.00 0.00 0.00 +GCC 171 20.00 28.00 33.00 19.00 0.00 0.00 +GCC 172 19.00 20.00 32.00 29.00 0.00 0.00 +GCC 173 24.50 16.50 33.50 25.50 0.00 0.00 +GCC 174 17.50 23.50 33.50 25.50 0.00 0.00 +GCC 175 33.50 17.50 35.50 13.50 0.00 0.00 +GCC 176 16.50 32.50 28.50 22.50 0.00 0.00 +GCC 177 19.00 22.00 27.00 32.00 0.00 0.00 +GCC 178 16.00 26.00 30.00 28.00 0.00 0.00 +GCC 179 18.00 18.00 22.00 42.00 0.00 0.00 +GCC 180 21.00 22.00 34.00 23.00 0.00 0.00 +GCC 181 20.50 19.50 35.50 24.50 0.00 0.00 +GCC 182 32.50 18.50 22.50 26.50 0.00 0.00 +GCC 183 24.50 13.50 28.50 33.50 0.00 0.00 +GCC 184 15.00 29.00 30.00 26.00 0.00 0.00 +GCC 185 15.00 32.00 33.00 20.00 0.00 0.00 +GCC 186 22.50 23.50 34.50 19.50 0.00 0.00 +GCC 187 19.00 14.00 40.00 27.00 0.00 0.00 +GCC 188 27.50 21.50 27.50 23.50 0.00 0.00 +GCC 189 17.00 22.00 34.00 27.00 0.00 0.00 +GCC 190 23.00 30.00 23.00 24.00 0.00 0.00 +GCC 191 25.00 22.00 28.00 25.00 0.00 0.00 +GCC 192 34.50 24.50 13.50 27.50 0.00 0.00 +GCC 193 18.50 25.50 25.50 30.50 0.00 0.00 +GCC 194 18.50 33.50 24.50 23.50 0.00 0.00 +GCC 195 16.00 26.00 23.00 35.00 0.00 0.00 +GCC 196 21.50 25.50 24.50 28.50 0.00 0.00 +GCC 197 20.00 21.00 23.00 36.00 0.00 0.00 +GCC 198 17.00 21.00 37.00 25.00 0.00 0.00 +GCC 199 20.50 18.50 25.50 35.50 0.00 0.00 +GCC 200 21.00 29.00 21.00 29.00 0.00 0.00 +GCC 201 27.00 21.00 23.00 29.00 0.00 0.00 +GCC 202 21.50 24.50 19.50 34.50 0.00 0.00 +GCC 203 21.50 24.50 26.50 27.50 0.00 0.00 +GCC 204 27.00 29.00 24.00 20.00 0.00 0.00 +GCC 205 19.50 21.50 22.50 36.50 0.00 0.00 +GCC 206 26.50 24.50 21.50 27.50 0.00 0.00 +GCC 207 22.50 21.50 19.50 36.50 0.00 0.00 +GCC 208 14.00 35.00 29.00 22.00 0.00 0.00 +GCC 209 16.00 23.00 12.00 49.00 0.00 0.00 +GCC 210 18.50 19.50 40.50 21.50 0.00 0.00 +GCC 211 26.00 20.00 22.00 32.00 0.00 0.00 +GCC 212 21.00 31.00 18.00 30.00 0.00 0.00 +GCC 213 24.00 15.00 31.00 30.00 0.00 0.00 +GCC 214 17.50 24.50 25.50 32.50 0.00 0.00 +GCC 215 26.00 24.00 23.00 27.00 0.00 0.00 +GCC 216 21.50 17.50 25.50 35.50 0.00 0.00 +GCC 217 26.00 29.00 17.00 28.00 0.00 0.00 +GCC 218 20.00 27.00 21.00 32.00 0.00 0.00 +GCC 219 17.00 21.00 21.00 41.00 0.00 0.00 +GCC 220 25.50 23.50 23.50 27.50 0.00 0.00 +GCC 221 21.50 23.50 20.50 34.50 0.00 0.00 +GCC 222 21.50 21.50 18.50 38.50 0.00 0.00 +GCC 223 20.00 27.00 28.00 25.00 0.00 0.00 +GCC 224 22.50 22.50 24.50 30.50 0.00 0.00 +GCC 225 14.50 35.50 30.50 19.50 0.00 0.00 +GCC 226 20.00 23.00 26.00 31.00 0.00 0.00 +GCC 227 20.50 24.50 23.50 31.50 0.00 0.00 +GCC 228 33.00 19.00 26.00 22.00 0.00 0.00 +GCC 229 22.50 24.50 18.50 34.50 0.00 0.00 +GCC 230 21.00 32.00 16.00 31.00 0.00 0.00 +GCC 231 23.00 28.00 30.00 19.00 0.00 0.00 +GCC 232 23.50 21.50 12.50 42.50 0.00 0.00 +GCC 233 21.00 27.00 25.00 27.00 0.00 0.00 +GCC 234 16.50 27.50 22.50 33.50 0.00 0.00 +GCC 235 20.00 15.00 28.00 37.00 0.00 0.00 +GCC 236 28.00 23.00 21.00 28.00 0.00 0.00 +GCC 237 20.50 19.50 22.50 37.50 0.00 0.00 +GCC 238 21.50 29.50 24.50 24.50 0.00 0.00 +GCC 239 20.00 8.00 17.00 55.00 0.00 0.00 +GCC 240 28.00 24.00 16.00 32.00 0.00 0.00 +GCC 241 22.50 22.50 16.50 38.50 0.00 0.00 +GCC 242 29.00 25.00 13.00 33.00 0.00 0.00 +GCC 243 22.50 15.50 23.50 38.50 0.00 0.00 +GCC 244 20.50 23.50 16.50 39.50 0.00 0.00 +GCC 245 28.00 23.00 19.00 30.00 0.00 0.00 +GCC 246 21.00 29.00 25.00 25.00 0.00 0.00 +GCC 247 32.00 14.00 13.00 41.00 0.00 0.00 +GCC 248 18.00 18.00 25.00 39.00 0.00 0.00 +GCC 249 25.00 23.00 21.00 31.00 0.00 0.00 +GCC 250 27.50 22.50 17.50 32.50 0.00 0.00 +GCC 251 13.50 20.50 36.50 29.50 0.00 0.00 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 251 200 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff --git a/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab new file mode 100644 index 00000000000..90cfc888533 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab @@ -0,0 +1,1138 @@ +# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_5.dat /tmp/tmpO1aTrb/files/000/dataset_4.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1bd20fd8 58ad2167 29883386 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. 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quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] +GCC 1 21.94 30.10 34.18 13.78 2.04 0.00 +GCC 2 30.00 16.00 11.00 43.00 0.00 0.00 +GCC 3 33.00 25.00 9.00 33.00 0.00 0.00 +GCC 4 17.00 29.00 13.00 41.00 0.00 0.00 +GCC 5 37.00 22.00 12.00 29.00 0.00 0.00 +GCC 6 36.00 26.00 17.00 21.00 0.00 0.00 +GCC 7 29.50 13.50 31.50 25.50 0.00 0.00 +GCC 8 50.50 14.50 19.50 15.50 0.00 0.00 +GCC 9 17.00 33.00 18.00 32.00 0.00 0.00 +GCC 10 37.00 14.00 21.00 28.00 0.00 0.00 +GCC 11 20.50 14.50 29.50 35.50 0.00 0.00 +GCC 12 30.00 24.00 22.00 24.00 0.00 0.00 +GCC 13 27.00 15.00 21.00 37.00 0.00 0.00 +GCC 14 24.24 22.22 26.26 27.27 1.01 0.00 +GCC 15 25.50 20.50 24.50 29.50 0.00 0.00 +GCC 16 31.00 15.00 20.00 34.00 0.00 0.00 +GCC 17 28.00 25.00 14.00 33.00 0.00 0.00 +GCC 18 30.50 28.50 19.50 21.50 0.00 0.00 +GCC 19 29.00 26.00 21.00 24.00 0.00 0.00 +GCC 20 22.50 23.50 17.50 36.50 0.00 0.00 +GCC 21 35.50 17.50 19.50 27.50 0.00 0.00 +GCC 22 37.50 28.50 15.50 18.50 0.00 0.00 +GCC 23 31.31 19.19 13.13 36.36 1.01 0.00 +GCC 24 37.00 12.00 22.00 29.00 0.00 0.00 +GCC 25 35.50 22.50 17.50 24.50 0.00 0.00 +GCC 26 33.50 18.50 15.50 32.50 0.00 0.00 +GCC 27 34.50 14.50 25.50 25.50 0.00 0.00 +GCC 28 31.00 14.00 24.00 31.00 0.00 0.00 +GCC 29 30.00 27.00 24.00 19.00 0.00 0.00 +GCC 30 31.00 20.00 14.00 35.00 0.00 0.00 +GCC 31 33.50 29.50 13.50 23.50 0.00 0.00 +GCC 32 42.50 20.50 19.50 17.50 0.00 0.00 +GCC 33 25.50 23.50 14.50 36.50 0.00 0.00 +GCC 34 39.50 16.50 20.50 23.50 0.00 0.00 +GCC 35 32.50 23.50 21.50 22.50 0.00 0.00 +GCC 36 42.00 25.00 16.00 17.00 0.00 0.00 +GCC 37 38.00 17.00 19.00 26.00 0.00 0.00 +GCC 38 24.00 26.00 25.00 25.00 0.00 0.00 +GCC 39 22.50 41.50 18.50 17.50 0.00 0.00 +GCC 40 32.00 16.00 21.00 31.00 0.00 0.00 +GCC 41 33.00 28.00 19.00 20.00 0.00 0.00 +GCC 42 30.50 25.50 19.50 24.50 0.00 0.00 +GCC 43 35.00 29.00 15.00 21.00 0.00 0.00 +GCC 44 20.00 27.00 22.00 31.00 0.00 0.00 +GCC 45 40.50 21.50 21.50 16.50 0.00 0.00 +GCC 46 26.50 20.50 22.50 30.50 0.00 0.00 +GCC 47 38.50 29.50 16.50 15.50 0.00 0.00 +GCC 48 27.50 24.50 17.50 30.50 0.00 0.00 +GCC 49 28.50 32.50 10.50 28.50 0.00 0.00 +GCC 50 46.50 20.50 9.50 23.50 0.00 0.00 +GCC 51 34.50 28.50 13.50 23.50 0.00 0.00 +GCC 52 41.50 23.50 20.50 14.50 0.00 0.00 +GCC 53 20.00 28.00 26.00 26.00 0.00 0.00 +GCC 54 31.50 18.50 24.50 25.50 0.00 0.00 +GCC 55 30.50 22.50 16.50 30.50 0.00 0.00 +GCC 56 33.50 22.50 13.50 30.50 0.00 0.00 +GCC 57 23.00 24.00 23.00 30.00 0.00 0.00 +GCC 58 25.00 37.00 19.00 19.00 0.00 0.00 +GCC 59 34.00 23.00 24.00 19.00 0.00 0.00 +GCC 60 29.00 28.00 17.00 26.00 0.00 0.00 +GCC 61 25.50 23.50 24.50 26.50 0.00 0.00 +GCC 62 31.50 22.50 16.50 29.50 0.00 0.00 +GCC 63 27.50 28.50 25.50 18.50 0.00 0.00 +GCC 64 33.50 21.50 25.50 19.50 0.00 0.00 +GCC 65 35.50 19.50 18.50 26.50 0.00 0.00 +GCC 66 34.00 25.00 15.00 26.00 0.00 0.00 +GCC 67 37.00 23.00 19.00 21.00 0.00 0.00 +GCC 68 36.50 29.50 13.50 20.50 0.00 0.00 +GCC 69 38.50 19.50 20.50 21.50 0.00 0.00 +GCC 70 38.50 16.50 18.50 26.50 0.00 0.00 +GCC 71 25.50 38.50 21.50 14.50 0.00 0.00 +GCC 72 29.00 29.00 25.00 17.00 0.00 0.00 +GCC 73 32.50 20.50 21.50 25.50 0.00 0.00 +GCC 74 28.50 32.50 12.50 26.50 0.00 0.00 +GCC 75 41.50 12.50 18.50 27.50 0.00 0.00 +GCC 76 24.50 29.50 23.50 22.50 0.00 0.00 +GCC 77 36.00 21.00 18.00 25.00 0.00 0.00 +GCC 78 27.00 34.00 22.00 17.00 0.00 0.00 +GCC 79 21.50 26.50 25.50 26.50 0.00 0.00 +GCC 80 34.00 19.00 28.00 19.00 0.00 0.00 +GCC 81 17.00 26.00 26.00 31.00 0.00 0.00 +GCC 82 31.00 30.00 23.00 16.00 0.00 0.00 +GCC 83 31.50 26.50 12.50 29.50 0.00 0.00 +GCC 84 19.00 41.00 21.00 19.00 0.00 0.00 +GCC 85 37.50 24.50 16.50 21.50 0.00 0.00 +GCC 86 15.00 48.00 15.00 22.00 0.00 0.00 +GCC 87 41.00 16.00 18.00 25.00 0.00 0.00 +GCC 88 23.50 27.50 27.50 21.50 0.00 0.00 +GCC 89 26.50 27.50 26.50 19.50 0.00 0.00 +GCC 90 18.50 23.50 24.50 33.50 0.00 0.00 +GCC 91 27.00 32.00 22.00 19.00 0.00 0.00 +GCC 92 23.50 17.50 27.50 31.50 0.00 0.00 +GCC 93 25.50 37.50 15.50 21.50 0.00 0.00 +GCC 94 27.00 17.00 24.00 32.00 0.00 0.00 +GCC 95 26.77 37.88 14.65 20.71 1.01 0.00 +GCC 96 29.50 25.50 16.50 28.50 0.00 0.00 +GCC 97 29.00 31.00 21.00 19.00 0.00 0.00 +GCC 98 18.18 33.33 22.22 26.26 1.01 0.00 +GCC 99 24.50 33.50 24.50 17.50 0.00 0.00 +GCC 100 24.50 16.50 24.50 34.50 0.00 0.00 +GCC 101 25.00 40.00 19.00 16.00 0.00 0.00 +GCC 102 17.50 17.50 32.50 32.50 0.00 0.00 +GCC 103 31.00 26.00 16.00 27.00 0.00 0.00 +GCC 104 26.50 29.50 20.50 23.50 0.00 0.00 +GCC 105 34.00 33.00 21.00 12.00 0.00 0.00 +GCC 106 23.00 31.00 26.00 20.00 0.00 0.00 +GCC 107 17.68 35.86 23.74 22.73 1.01 0.00 +GCC 108 24.75 30.81 23.74 20.71 1.01 0.00 +GCC 109 17.00 31.00 22.00 30.00 0.00 0.00 +GCC 110 16.16 35.35 24.24 24.24 1.01 0.00 +GCC 111 24.24 32.32 23.23 20.20 1.01 0.00 +GCC 112 37.37 28.28 16.16 18.18 1.01 0.00 +GCC 113 19.70 22.73 32.83 24.75 1.01 0.00 +GCC 114 17.00 31.00 35.00 17.00 0.00 0.00 +GCC 115 29.50 24.50 23.50 22.50 0.00 0.00 +GCC 116 22.00 30.00 34.00 14.00 0.00 0.00 +GCC 117 27.00 23.00 19.00 31.00 0.00 0.00 +GCC 118 25.50 14.50 34.50 25.50 0.00 0.00 +GCC 119 22.50 34.50 20.50 22.50 0.00 0.00 +GCC 120 17.50 24.50 26.50 31.50 0.00 0.00 +GCC 121 27.78 33.84 22.73 15.66 1.01 0.00 +GCC 122 17.00 23.00 25.00 35.00 0.00 0.00 +GCC 123 23.50 46.50 11.50 18.50 0.00 0.00 +GCC 124 9.00 32.00 34.00 25.00 0.00 0.00 +GCC 125 24.00 27.00 19.00 30.00 0.00 0.00 +GCC 126 26.00 17.00 28.00 29.00 0.00 0.00 +GCC 127 26.50 16.50 21.50 35.50 0.00 0.00 +GCC 128 18.00 34.00 31.00 17.00 0.00 0.00 +GCC 129 25.50 25.50 27.50 21.50 0.00 0.00 +GCC 130 25.00 20.00 22.00 33.00 0.00 0.00 +GCC 131 17.50 39.50 24.50 18.50 0.00 0.00 +GCC 132 21.00 28.00 23.00 28.00 0.00 0.00 +GCC 133 13.50 31.50 35.50 19.50 0.00 0.00 +GCC 134 24.50 19.50 30.50 25.50 0.00 0.00 +GCC 135 16.50 23.50 30.50 29.50 0.00 0.00 +GCC 136 28.00 32.00 15.00 25.00 0.00 0.00 +GCC 137 22.50 21.50 30.50 25.50 0.00 0.00 +GCC 138 14.50 34.50 24.50 26.50 0.00 0.00 +GCC 139 20.50 29.50 24.50 25.50 0.00 0.00 +GCC 140 17.00 23.00 30.00 30.00 0.00 0.00 +GCC 141 20.50 23.50 25.50 30.50 0.00 0.00 +GCC 142 18.00 29.00 38.00 15.00 0.00 0.00 +GCC 143 22.00 24.00 27.00 27.00 0.00 0.00 +GCC 144 21.50 30.50 26.50 21.50 0.00 0.00 +GCC 145 22.00 21.00 29.00 28.00 0.00 0.00 +GCC 146 25.00 16.00 39.00 20.00 0.00 0.00 +GCC 147 26.50 22.50 30.50 20.50 0.00 0.00 +GCC 148 12.50 28.50 36.50 22.50 0.00 0.00 +GCC 149 26.50 23.50 23.50 26.50 0.00 0.00 +GCC 150 14.00 29.00 24.00 33.00 0.00 0.00 +GCC 151 19.50 30.50 32.50 17.50 0.00 0.00 +GCC 152 18.50 17.50 29.50 34.50 0.00 0.00 +GCC 153 22.50 22.50 31.50 23.50 0.00 0.00 +GCC 154 22.00 21.00 29.00 28.00 0.00 0.00 +GCC 155 21.00 26.00 19.00 34.00 0.00 0.00 +GCC 156 14.50 23.50 35.50 26.50 0.00 0.00 +GCC 157 22.00 31.00 23.00 24.00 0.00 0.00 +GCC 158 22.50 29.50 24.50 23.50 0.00 0.00 +GCC 159 17.50 12.50 46.50 23.50 0.00 0.00 +GCC 160 24.50 26.50 26.50 22.50 0.00 0.00 +GCC 161 13.00 23.00 45.00 19.00 0.00 0.00 +GCC 162 31.50 16.50 22.50 29.50 0.00 0.00 +GCC 163 19.50 21.50 35.50 23.50 0.00 0.00 +GCC 164 29.00 18.00 21.00 32.00 0.00 0.00 +GCC 165 14.50 17.50 35.50 32.50 0.00 0.00 +GCC 166 17.50 37.50 28.50 16.50 0.00 0.00 +GCC 167 16.50 21.50 31.50 30.50 0.00 0.00 +GCC 168 14.00 25.00 30.00 31.00 0.00 0.00 +GCC 169 18.50 20.50 23.50 37.50 0.00 0.00 +GCC 170 19.00 23.00 28.00 30.00 0.00 0.00 +GCC 171 20.00 28.00 33.00 19.00 0.00 0.00 +GCC 172 19.00 20.00 32.00 29.00 0.00 0.00 +GCC 173 24.50 16.50 33.50 25.50 0.00 0.00 +GCC 174 17.50 23.50 33.50 25.50 0.00 0.00 +GCC 175 33.50 17.50 35.50 13.50 0.00 0.00 +GCC 176 16.50 32.50 28.50 22.50 0.00 0.00 +GCC 177 19.00 22.00 27.00 32.00 0.00 0.00 +GCC 178 16.00 26.00 30.00 28.00 0.00 0.00 +GCC 179 18.00 18.00 22.00 42.00 0.00 0.00 +GCC 180 21.00 22.00 34.00 23.00 0.00 0.00 +GCC 181 20.50 19.50 35.50 24.50 0.00 0.00 +GCC 182 32.50 18.50 22.50 26.50 0.00 0.00 +GCC 183 24.50 13.50 28.50 33.50 0.00 0.00 +GCC 184 15.00 29.00 30.00 26.00 0.00 0.00 +GCC 185 15.00 32.00 33.00 20.00 0.00 0.00 +GCC 186 22.50 23.50 34.50 19.50 0.00 0.00 +GCC 187 19.00 14.00 40.00 27.00 0.00 0.00 +GCC 188 27.50 21.50 27.50 23.50 0.00 0.00 +GCC 189 17.00 22.00 34.00 27.00 0.00 0.00 +GCC 190 23.00 30.00 23.00 24.00 0.00 0.00 +GCC 191 25.00 22.00 28.00 25.00 0.00 0.00 +GCC 192 34.50 24.50 13.50 27.50 0.00 0.00 +GCC 193 18.50 25.50 25.50 30.50 0.00 0.00 +GCC 194 18.50 33.50 24.50 23.50 0.00 0.00 +GCC 195 16.00 26.00 23.00 35.00 0.00 0.00 +GCC 196 21.50 25.50 24.50 28.50 0.00 0.00 +GCC 197 20.00 21.00 23.00 36.00 0.00 0.00 +GCC 198 17.00 21.00 37.00 25.00 0.00 0.00 +GCC 199 20.50 18.50 25.50 35.50 0.00 0.00 +GCC 200 21.00 29.00 21.00 29.00 0.00 0.00 +GCC 201 27.00 21.00 23.00 29.00 0.00 0.00 +GCC 202 21.50 24.50 19.50 34.50 0.00 0.00 +GCC 203 21.50 24.50 26.50 27.50 0.00 0.00 +GCC 204 27.00 29.00 24.00 20.00 0.00 0.00 +GCC 205 19.50 21.50 22.50 36.50 0.00 0.00 +GCC 206 26.50 24.50 21.50 27.50 0.00 0.00 +GCC 207 22.50 21.50 19.50 36.50 0.00 0.00 +GCC 208 14.00 35.00 29.00 22.00 0.00 0.00 +GCC 209 16.00 23.00 12.00 49.00 0.00 0.00 +GCC 210 18.50 19.50 40.50 21.50 0.00 0.00 +GCC 211 26.00 20.00 22.00 32.00 0.00 0.00 +GCC 212 21.00 31.00 18.00 30.00 0.00 0.00 +GCC 213 24.00 15.00 31.00 30.00 0.00 0.00 +GCC 214 17.50 24.50 25.50 32.50 0.00 0.00 +GCC 215 26.00 24.00 23.00 27.00 0.00 0.00 +GCC 216 21.50 17.50 25.50 35.50 0.00 0.00 +GCC 217 26.00 29.00 17.00 28.00 0.00 0.00 +GCC 218 20.00 27.00 21.00 32.00 0.00 0.00 +GCC 219 17.00 21.00 21.00 41.00 0.00 0.00 +GCC 220 25.50 23.50 23.50 27.50 0.00 0.00 +GCC 221 21.50 23.50 20.50 34.50 0.00 0.00 +GCC 222 21.50 21.50 18.50 38.50 0.00 0.00 +GCC 223 20.00 27.00 28.00 25.00 0.00 0.00 +GCC 224 22.50 22.50 24.50 30.50 0.00 0.00 +GCC 225 14.50 35.50 30.50 19.50 0.00 0.00 +GCC 226 20.00 23.00 26.00 31.00 0.00 0.00 +GCC 227 20.50 24.50 23.50 31.50 0.00 0.00 +GCC 228 33.00 19.00 26.00 22.00 0.00 0.00 +GCC 229 22.50 24.50 18.50 34.50 0.00 0.00 +GCC 230 21.00 32.00 16.00 31.00 0.00 0.00 +GCC 231 23.00 28.00 30.00 19.00 0.00 0.00 +GCC 232 23.50 21.50 12.50 42.50 0.00 0.00 +GCC 233 21.00 27.00 25.00 27.00 0.00 0.00 +GCC 234 16.50 27.50 22.50 33.50 0.00 0.00 +GCC 235 20.00 15.00 28.00 37.00 0.00 0.00 +GCC 236 28.00 23.00 21.00 28.00 0.00 0.00 +GCC 237 20.50 19.50 22.50 37.50 0.00 0.00 +GCC 238 21.50 29.50 24.50 24.50 0.00 0.00 +GCC 239 20.00 8.00 17.00 55.00 0.00 0.00 +GCC 240 28.00 24.00 16.00 32.00 0.00 0.00 +GCC 241 22.50 22.50 16.50 38.50 0.00 0.00 +GCC 242 29.00 25.00 13.00 33.00 0.00 0.00 +GCC 243 22.50 15.50 23.50 38.50 0.00 0.00 +GCC 244 20.50 23.50 16.50 39.50 0.00 0.00 +GCC 245 28.00 23.00 19.00 30.00 0.00 0.00 +GCC 246 21.00 29.00 25.00 25.00 0.00 0.00 +GCC 247 32.00 14.00 13.00 41.00 0.00 0.00 +GCC 248 18.00 18.00 25.00 39.00 0.00 0.00 +GCC 249 25.00 23.00 21.00 31.00 0.00 0.00 +GCC 250 27.50 22.50 17.50 32.50 0.00 0.00 +GCC 251 13.50 20.50 36.50 29.50 0.00 0.00 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 251 200 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff --git a/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__gcc.tab b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__gcc.tab new file mode 100644 index 00000000000..a1fd54eca93 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__gcc.tab @@ -0,0 +1,252 @@ +# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent) +1 21.94 30.10 34.18 13.78 2.04 0.00 +2 30.00 16.00 11.00 43.00 0.00 0.00 +3 33.00 25.00 9.00 33.00 0.00 0.00 +4 17.00 29.00 13.00 41.00 0.00 0.00 +5 37.00 22.00 12.00 29.00 0.00 0.00 +6 36.00 26.00 17.00 21.00 0.00 0.00 +7 29.50 13.50 31.50 25.50 0.00 0.00 +8 50.50 14.50 19.50 15.50 0.00 0.00 +9 17.00 33.00 18.00 32.00 0.00 0.00 +10 37.00 14.00 21.00 28.00 0.00 0.00 +11 20.50 14.50 29.50 35.50 0.00 0.00 +12 30.00 24.00 22.00 24.00 0.00 0.00 +13 27.00 15.00 21.00 37.00 0.00 0.00 +14 24.24 22.22 26.26 27.27 1.01 0.00 +15 25.50 20.50 24.50 29.50 0.00 0.00 +16 31.00 15.00 20.00 34.00 0.00 0.00 +17 28.00 25.00 14.00 33.00 0.00 0.00 +18 30.50 28.50 19.50 21.50 0.00 0.00 +19 29.00 26.00 21.00 24.00 0.00 0.00 +20 22.50 23.50 17.50 36.50 0.00 0.00 +21 35.50 17.50 19.50 27.50 0.00 0.00 +22 37.50 28.50 15.50 18.50 0.00 0.00 +23 31.31 19.19 13.13 36.36 1.01 0.00 +24 37.00 12.00 22.00 29.00 0.00 0.00 +25 35.50 22.50 17.50 24.50 0.00 0.00 +26 33.50 18.50 15.50 32.50 0.00 0.00 +27 34.50 14.50 25.50 25.50 0.00 0.00 +28 31.00 14.00 24.00 31.00 0.00 0.00 +29 30.00 27.00 24.00 19.00 0.00 0.00 +30 31.00 20.00 14.00 35.00 0.00 0.00 +31 33.50 29.50 13.50 23.50 0.00 0.00 +32 42.50 20.50 19.50 17.50 0.00 0.00 +33 25.50 23.50 14.50 36.50 0.00 0.00 +34 39.50 16.50 20.50 23.50 0.00 0.00 +35 32.50 23.50 21.50 22.50 0.00 0.00 +36 42.00 25.00 16.00 17.00 0.00 0.00 +37 38.00 17.00 19.00 26.00 0.00 0.00 +38 24.00 26.00 25.00 25.00 0.00 0.00 +39 22.50 41.50 18.50 17.50 0.00 0.00 +40 32.00 16.00 21.00 31.00 0.00 0.00 +41 33.00 28.00 19.00 20.00 0.00 0.00 +42 30.50 25.50 19.50 24.50 0.00 0.00 +43 35.00 29.00 15.00 21.00 0.00 0.00 +44 20.00 27.00 22.00 31.00 0.00 0.00 +45 40.50 21.50 21.50 16.50 0.00 0.00 +46 26.50 20.50 22.50 30.50 0.00 0.00 +47 38.50 29.50 16.50 15.50 0.00 0.00 +48 27.50 24.50 17.50 30.50 0.00 0.00 +49 28.50 32.50 10.50 28.50 0.00 0.00 +50 46.50 20.50 9.50 23.50 0.00 0.00 +51 34.50 28.50 13.50 23.50 0.00 0.00 +52 41.50 23.50 20.50 14.50 0.00 0.00 +53 20.00 28.00 26.00 26.00 0.00 0.00 +54 31.50 18.50 24.50 25.50 0.00 0.00 +55 30.50 22.50 16.50 30.50 0.00 0.00 +56 33.50 22.50 13.50 30.50 0.00 0.00 +57 23.00 24.00 23.00 30.00 0.00 0.00 +58 25.00 37.00 19.00 19.00 0.00 0.00 +59 34.00 23.00 24.00 19.00 0.00 0.00 +60 29.00 28.00 17.00 26.00 0.00 0.00 +61 25.50 23.50 24.50 26.50 0.00 0.00 +62 31.50 22.50 16.50 29.50 0.00 0.00 +63 27.50 28.50 25.50 18.50 0.00 0.00 +64 33.50 21.50 25.50 19.50 0.00 0.00 +65 35.50 19.50 18.50 26.50 0.00 0.00 +66 34.00 25.00 15.00 26.00 0.00 0.00 +67 37.00 23.00 19.00 21.00 0.00 0.00 +68 36.50 29.50 13.50 20.50 0.00 0.00 +69 38.50 19.50 20.50 21.50 0.00 0.00 +70 38.50 16.50 18.50 26.50 0.00 0.00 +71 25.50 38.50 21.50 14.50 0.00 0.00 +72 29.00 29.00 25.00 17.00 0.00 0.00 +73 32.50 20.50 21.50 25.50 0.00 0.00 +74 28.50 32.50 12.50 26.50 0.00 0.00 +75 41.50 12.50 18.50 27.50 0.00 0.00 +76 24.50 29.50 23.50 22.50 0.00 0.00 +77 36.00 21.00 18.00 25.00 0.00 0.00 +78 27.00 34.00 22.00 17.00 0.00 0.00 +79 21.50 26.50 25.50 26.50 0.00 0.00 +80 34.00 19.00 28.00 19.00 0.00 0.00 +81 17.00 26.00 26.00 31.00 0.00 0.00 +82 31.00 30.00 23.00 16.00 0.00 0.00 +83 31.50 26.50 12.50 29.50 0.00 0.00 +84 19.00 41.00 21.00 19.00 0.00 0.00 +85 37.50 24.50 16.50 21.50 0.00 0.00 +86 15.00 48.00 15.00 22.00 0.00 0.00 +87 41.00 16.00 18.00 25.00 0.00 0.00 +88 23.50 27.50 27.50 21.50 0.00 0.00 +89 26.50 27.50 26.50 19.50 0.00 0.00 +90 18.50 23.50 24.50 33.50 0.00 0.00 +91 27.00 32.00 22.00 19.00 0.00 0.00 +92 23.50 17.50 27.50 31.50 0.00 0.00 +93 25.50 37.50 15.50 21.50 0.00 0.00 +94 27.00 17.00 24.00 32.00 0.00 0.00 +95 26.77 37.88 14.65 20.71 1.01 0.00 +96 29.50 25.50 16.50 28.50 0.00 0.00 +97 29.00 31.00 21.00 19.00 0.00 0.00 +98 18.18 33.33 22.22 26.26 1.01 0.00 +99 24.50 33.50 24.50 17.50 0.00 0.00 +100 24.50 16.50 24.50 34.50 0.00 0.00 +101 25.00 40.00 19.00 16.00 0.00 0.00 +102 17.50 17.50 32.50 32.50 0.00 0.00 +103 31.00 26.00 16.00 27.00 0.00 0.00 +104 26.50 29.50 20.50 23.50 0.00 0.00 +105 34.00 33.00 21.00 12.00 0.00 0.00 +106 23.00 31.00 26.00 20.00 0.00 0.00 +107 17.68 35.86 23.74 22.73 1.01 0.00 +108 24.75 30.81 23.74 20.71 1.01 0.00 +109 17.00 31.00 22.00 30.00 0.00 0.00 +110 16.16 35.35 24.24 24.24 1.01 0.00 +111 24.24 32.32 23.23 20.20 1.01 0.00 +112 37.37 28.28 16.16 18.18 1.01 0.00 +113 19.70 22.73 32.83 24.75 1.01 0.00 +114 17.00 31.00 35.00 17.00 0.00 0.00 +115 29.50 24.50 23.50 22.50 0.00 0.00 +116 22.00 30.00 34.00 14.00 0.00 0.00 +117 27.00 23.00 19.00 31.00 0.00 0.00 +118 25.50 14.50 34.50 25.50 0.00 0.00 +119 22.50 34.50 20.50 22.50 0.00 0.00 +120 17.50 24.50 26.50 31.50 0.00 0.00 +121 27.78 33.84 22.73 15.66 1.01 0.00 +122 17.00 23.00 25.00 35.00 0.00 0.00 +123 23.50 46.50 11.50 18.50 0.00 0.00 +124 9.00 32.00 34.00 25.00 0.00 0.00 +125 24.00 27.00 19.00 30.00 0.00 0.00 +126 26.00 17.00 28.00 29.00 0.00 0.00 +127 26.50 16.50 21.50 35.50 0.00 0.00 +128 18.00 34.00 31.00 17.00 0.00 0.00 +129 25.50 25.50 27.50 21.50 0.00 0.00 +130 25.00 20.00 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22.50 21.50 19.50 36.50 0.00 0.00 +208 14.00 35.00 29.00 22.00 0.00 0.00 +209 16.00 23.00 12.00 49.00 0.00 0.00 +210 18.50 19.50 40.50 21.50 0.00 0.00 +211 26.00 20.00 22.00 32.00 0.00 0.00 +212 21.00 31.00 18.00 30.00 0.00 0.00 +213 24.00 15.00 31.00 30.00 0.00 0.00 +214 17.50 24.50 25.50 32.50 0.00 0.00 +215 26.00 24.00 23.00 27.00 0.00 0.00 +216 21.50 17.50 25.50 35.50 0.00 0.00 +217 26.00 29.00 17.00 28.00 0.00 0.00 +218 20.00 27.00 21.00 32.00 0.00 0.00 +219 17.00 21.00 21.00 41.00 0.00 0.00 +220 25.50 23.50 23.50 27.50 0.00 0.00 +221 21.50 23.50 20.50 34.50 0.00 0.00 +222 21.50 21.50 18.50 38.50 0.00 0.00 +223 20.00 27.00 28.00 25.00 0.00 0.00 +224 22.50 22.50 24.50 30.50 0.00 0.00 +225 14.50 35.50 30.50 19.50 0.00 0.00 +226 20.00 23.00 26.00 31.00 0.00 0.00 +227 20.50 24.50 23.50 31.50 0.00 0.00 +228 33.00 19.00 26.00 22.00 0.00 0.00 +229 22.50 24.50 18.50 34.50 0.00 0.00 +230 21.00 32.00 16.00 31.00 0.00 0.00 +231 23.00 28.00 30.00 19.00 0.00 0.00 +232 23.50 21.50 12.50 42.50 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b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__mpc.tab @@ -0,0 +1,253 @@ +# Columns correspond to qualities, rows to cycles. 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1 1 3 2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__sn.tab b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__sn.tab new file mode 100644 index 00000000000..605df46e7a1 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2__sn.tab @@ -0,0 +1,33 @@ +# Summary Numbers + +raw total sequences: 200 +filtered sequences: 0 +sequences: 200 +is sorted: 1 +1st fragments: 100 +last fragments: 100 +reads mapped: 25 +reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +reads unmapped: 175 +reads properly paired: 0 # proper-pair bit set +reads paired: 200 # paired-end technology bit set +reads duplicated: 0 # PCR or optical duplicate bit set +reads MQ0: 6 # mapped and MQ=0 +reads QC failed: 0 +non-primary alignments: 0 +total length: 50200 # ignores clipping +bases mapped: 6275 # ignores clipping +bases mapped (cigar): 6275 # more accurate +bases trimmed: 0 +bases duplicated: 0 +mismatches: 591 # from NM fields +error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +average length: 251 +maximum length: 251 +average quality: 34.7 +insert size average: 0.0 +insert size standard deviation: 0.0 +inward oriented pairs: 0 +outward oriented pairs: 0 +pairs with other orientation: 0 +pairs on different chromosomes: 0 diff --git a/tool_collections/samtools/samtools_stats/test-data/samtools_stats_ref.fa b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_ref.fa new file mode 100644 index 00000000000..a4b24136e8e --- /dev/null +++ b/tool_collections/samtools/samtools_stats/test-data/samtools_stats_ref.fa @@ -0,0 +1,239 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG + diff --git a/tool_collections/samtools/samtools_stats/tool-data/fasta_indexes.loc.sample b/tool_collections/samtools/samtools_stats/tool-data/fasta_indexes.loc.sample new file mode 100644 index 00000000000..fd8fb70ac28 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/tool-data/fasta_indexes.loc.sample @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff --git a/tool_collections/samtools/samtools_stats/tool_data_table_conf.xml.sample b/tool_collections/samtools/samtools_stats/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..c34ade01890 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/tool_data_table_conf.xml.sample @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff --git a/tool_collections/vcflib/LICENSE b/tool_collections/vcflib/LICENSE new file mode 100644 index 00000000000..d176cde6c50 --- /dev/null +++ b/tool_collections/vcflib/LICENSE @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2014 Anton Nekrutenko + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/tool_collections/vcflib/README.rst b/tool_collections/vcflib/README.rst new file mode 100644 index 00000000000..d80c24d0e94 --- /dev/null +++ b/tool_collections/vcflib/README.rst @@ -0,0 +1,9 @@ +vcflib-tools +============ + +A collection of Galaxy wrappers for vcflib utilities. This is a +development copy of the tools that exist in the Galaxy Tool Shed +(http://usegalaxy.org/toolshed). + +Because vcflib can only be reliably compiled on Linux platforms at this +time these wrappers make this assumption. diff --git a/tool_collections/vcflib/macros.xml b/tool_collections/vcflib/macros.xml new file mode 100644 index 00000000000..f5de643d57c --- /dev/null +++ b/tool_collections/vcflib/macros.xml @@ -0,0 +1,29 @@ + + + + vcflib + + + + + + + + + 1.0.0_rc1 + + + +@misc{Garrison2015, + author = {Garrison, Erik}, + year = {2015}, + title = {vcflib}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ekg/vcflib}, +} + + + + is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + diff --git a/tool_collections/vcflib/tool-data/fasta_indexes.loc.sample b/tool_collections/vcflib/tool-data/fasta_indexes.loc.sample new file mode 100644 index 00000000000..fd8fb70ac28 --- /dev/null +++ b/tool_collections/vcflib/tool-data/fasta_indexes.loc.sample @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff --git a/tool_collections/vcflib/tool-data/tool_data_table_conf.xml.sample b/tool_collections/vcflib/tool-data/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..9111f18a24b --- /dev/null +++ b/tool_collections/vcflib/tool-data/tool_data_table_conf.xml.sample @@ -0,0 +1,8 @@ + + + + + value, dbkey, name, path + +
+ diff --git a/tool_collections/vcflib/vcf2tsv/.shed.yml b/tool_collections/vcflib/vcf2tsv/.shed.yml new file mode 100644 index 00000000000..46766cec405 --- /dev/null +++ b/tool_collections/vcflib/vcf2tsv/.shed.yml @@ -0,0 +1,14 @@ +categories: +- Variant Analysis +- Convert Formats +description: Converts VCF files into tab-delimited format +homepage_url: https://github.com/ekg/vcflib +long_description: | + Converts stdin or given VCF file to tab-delimited format, using + null string to replace empty values in the table. Specifying -g will output one + line per sample with genotype information. A part of the vcflib utilities developed + by Erik Garrison (https://github.com/ekg/vcflib). +name: vcf2tsv +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv +type: unrestricted diff --git a/tool_collections/vcflib/vcf2tsv/macros.xml b/tool_collections/vcflib/vcf2tsv/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcf2tsv/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcf2tsv/test-data/vcf2tsv-test1.tab b/tool_collections/vcflib/vcf2tsv/test-data/vcf2tsv-test1.tab new file mode 100644 index 00000000000..30a213d7fe2 --- /dev/null +++ b/tool_collections/vcflib/vcf2tsv/test-data/vcf2tsv-test1.tab @@ -0,0 +1,28 @@ +CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DP NS DB H2 SAMPLE DP GQ GT HQ +19 111 . A C 9.6 . . . . . . . 0 0 NA00001 . . 0|0 10,10 +19 111 . A C 9.6 . . . . . . . 0 0 NA00002 . . 0|0 10,10 +19 111 . A C 9.6 . . . . . . . 0 0 NA00003 . . 0/1 3,3 +19 112 . A G 10 . . . . . . . 0 0 NA00001 . . 0|0 10,10 +19 112 . A G 10 . . . . . . . 0 0 NA00002 . . 0|0 10,10 +19 112 . A G 10 . . . . . . . 0 0 NA00003 . . 0/1 3,3 +20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 NA00001 1 48 0|0 51,51 +20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 NA00002 8 48 1|0 51,51 +20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 NA00003 5 43 1/1 .,. +20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 NA00001 3 49 0|0 58,50 +20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 NA00002 5 3 0|1 65,3 +20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 NA00003 3 41 0/0 .,. +20 1110696 rs6040355 A G,T 67 PASS T . 0.333,0.667 . 10 2 1 0 NA00001 6 21 1|2 23,27 +20 1110696 rs6040355 A G,T 67 PASS T . 0.333,0.667 . 10 2 1 0 NA00002 0 2 2|1 18,2 +20 1110696 rs6040355 A G,T 67 PASS T . 0.333,0.667 . 10 2 1 0 NA00003 4 35 2/2 .,. +20 1230237 . T . 47 PASS T . . . 13 3 0 0 NA00001 . 54 0|0 56,60 +20 1230237 . T . 47 PASS T . . . 13 3 0 0 NA00002 4 48 0|0 51,51 +20 1230237 . T . 47 PASS T . . . 13 3 0 0 NA00003 2 61 0/0 .,. +20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00001 4 . 0/1 . +20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00002 2 17 0/2 . +20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00003 3 40 1/1 . +20 1235237 . T . 0 . . . . . . . 0 0 NA00001 . . 0/0 . +20 1235237 . T . 0 . . . . . . . 0 0 NA00002 . . 0|0 . +20 1235237 . T . 0 . . . . . . . 0 0 NA00003 . . ./. . +X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00001 . . 0 . +X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00002 . . 0/1 . +X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00003 . . 0|2 . diff --git a/tool_collections/vcflib/vcf2tsv/test-data/vcf2tsv-test2.tab b/tool_collections/vcflib/vcf2tsv/test-data/vcf2tsv-test2.tab new file mode 100644 index 00000000000..2169204f24d --- /dev/null +++ b/tool_collections/vcflib/vcf2tsv/test-data/vcf2tsv-test2.tab @@ -0,0 +1,13 @@ +CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DP NS DB H2 +19 111 . A C 9.6 . . . . . . . 0 0 +19 112 . A G 10 . . . . . . . 0 0 +20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 +20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 +20 1110696 rs6040355 A G 67 PASS T . 0.333 . 10 2 1 0 +20 1110696 rs6040355 A T 67 PASS T . 0.667 . 10 2 1 0 +20 1230237 . T . 47 PASS T . . . 13 3 0 0 +20 1234567 microsat1 G GA 50 PASS G 3 . 6 9 3 0 0 +20 1234567 microsat1 G GAC 50 PASS G 1 . 6 9 3 0 0 +20 1235237 . T . 0 . . . . . . . 0 0 +X 10 rsTest AC A 10 PASS . . . . . . 0 0 +X 10 rsTest AC ATG 10 PASS . . . . . . 0 0 diff --git a/tool_collections/vcflib/vcf2tsv/test-data/vcflib.vcf b/tool_collections/vcflib/vcf2tsv/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcf2tsv/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcf2tsv/vcf2tsv.xml b/tool_collections/vcflib/vcf2tsv/vcf2tsv.xml new file mode 100644 index 00000000000..90aa4c5206e --- /dev/null +++ b/tool_collections/vcflib/vcf2tsv/vcf2tsv.xml @@ -0,0 +1,45 @@ + + Convert VCF data into TAB-delimited format + + macros.xml + + + + vcf2tsv ${g_option} -n '${null_filler}' '${input}' > '${out_file1}' + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table. +Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information. + +---- + +Vcf2Tsv @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfaddinfo/.shed.yml b/tool_collections/vcflib/vcfaddinfo/.shed.yml new file mode 100644 index 00000000000..1e25fd2a5c8 --- /dev/null +++ b/tool_collections/vcflib/vcfaddinfo/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: Adds info fields from the second dataset which are not present in the + first dataset. +homepage_url: https://github.com/ekg/vcflib +long_description: | + Adds info fields from the second dataset which are not present in the first dataset. +name: vcfaddinfo +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo +type: unrestricted diff --git a/tool_collections/vcflib/vcfaddinfo/macros.xml b/tool_collections/vcflib/vcfaddinfo/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfaddinfo/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfaddinfo/test-data/vcfaddinfo-input1.vcf b/tool_collections/vcflib/vcfaddinfo/test-data/vcfaddinfo-input1.vcf new file mode 100644 index 00000000000..f0aa4c60979 --- /dev/null +++ b/tool_collections/vcflib/vcfaddinfo/test-data/vcfaddinfo-input1.vcf @@ -0,0 +1,24 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS NS=3;AF=0.5;DB;H2 GT:GQ:HQ 0|0:48:51,51 1|0:48:51,51 1/1:43:.,. +20 17330 . T A 3 q10 NS=3;AF=0.017 GT:GQ:HQ 0|0:49:58,50 0|1:3:65,3 0/0:41:.,. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfaddinfo/test-data/vcfaddinfo-test1.vcf b/tool_collections/vcflib/vcfaddinfo/test-data/vcfaddinfo-test1.vcf new file mode 100644 index 00000000000..c782c8750e7 --- /dev/null +++ b/tool_collections/vcflib/vcfaddinfo/test-data/vcfaddinfo-test1.vcf @@ -0,0 +1,25 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:HQ 0|0:48:51,51 1|0:48:51,51 1/1:43:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:HQ 0|0:49:58,50 0|1:3:65,3 0/0:41:.,. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfaddinfo/test-data/vcflib.vcf b/tool_collections/vcflib/vcfaddinfo/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfaddinfo/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfaddinfo/vcfaddinfo.xml b/tool_collections/vcflib/vcfaddinfo/vcfaddinfo.xml new file mode 100644 index 00000000000..8d4c52912a4 --- /dev/null +++ b/tool_collections/vcflib/vcfaddinfo/vcfaddinfo.xml @@ -0,0 +1,32 @@ + + Adds info fields from the second dataset which are not present in the first dataset + + macros.xml + + + + vcfaddinfo "${input1}" "${input2}" > "${out_file1}" + + + + + + + + + + + + + + + + +Adds info fields from the second dataset which are not present in the first dataset. + +----- + +Vcfaddinfo @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfallelicprimitives/.shed.yml b/tool_collections/vcflib/vcfallelicprimitives/.shed.yml new file mode 100644 index 00000000000..0d6ae31de22 --- /dev/null +++ b/tool_collections/vcflib/vcfallelicprimitives/.shed.yml @@ -0,0 +1,14 @@ +categories: +- Variant Analysis +description: Splits alleleic primitives (gaps or mismatches) into multiple VCF lines +homepage_url: https://github.com/ekg/vcflib +long_description: | + If multiple alleleic primitives (gaps or mismatches) are specified + in a single VCF record, this tools splits the record into multiple lines, but drops + all INFO fields. "Pure" MNPs are split into multiple SNPs unless the -m flag is + provided. Genotypes are phased where complex alleles have been decomposed, provided + genotypes in the input. +name: vcfallelicprimitives +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives +type: unrestricted diff --git a/tool_collections/vcflib/vcfallelicprimitives/macros.xml b/tool_collections/vcflib/vcfallelicprimitives/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfallelicprimitives/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfallelicprimitives/test-data/vcfallelicprimitives-test1.vcf b/tool_collections/vcflib/vcfallelicprimitives/test-data/vcfallelicprimitives-test1.vcf new file mode 100644 index 00000000000..21a10473514 --- /dev/null +++ b/tool_collections/vcflib/vcfallelicprimitives/test-data/vcfallelicprimitives-test1.vcf @@ -0,0 +1,35 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 . A G,T 67 PASS AF=0.333,0.667;LEN=1,1;TYPE=snp,snp;Split primitives GT 1|2 2|1 2|2 +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 . G GA,GAC 50 PASS AC=3,1;LEN=1,2;TYPE=ins,ins;Split primitives GT 0|1 0|2 1|1 +20 1235237 . T . 0 . . GT 0/0 0|0 ./. +X 10 . AC ATC,A 10 PASS LEN=1,1;TYPE=ins,del;Split primitives GT 0 0|2 0|1 +X 11 . C G 10 PASS LEN=1;TYPE=snp;Split primitives GT 0 0|0 0|1 diff --git a/tool_collections/vcflib/vcfallelicprimitives/test-data/vcflib.vcf b/tool_collections/vcflib/vcfallelicprimitives/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfallelicprimitives/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfallelicprimitives/vcfallelicprimitives.xml b/tool_collections/vcflib/vcfallelicprimitives/vcfallelicprimitives.xml new file mode 100644 index 00000000000..c5498fbbc1a --- /dev/null +++ b/tool_collections/vcflib/vcfallelicprimitives/vcfallelicprimitives.xml @@ -0,0 +1,62 @@ + + + Split alleleic primitives (gaps or mismatches) into multiple VCF lines + + macros.xml + + + + + cat "${input}" | vcfallelicprimitives + ${m_option} + -t "${t_option}" + -L "${max_length}" + $keep_info + $keep_geno > "${out_file1}" + + + + + + + + + + + + + + + + + + + + +If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields. +"Pure" MNPs are split into multiple SNPs unless the -m flag is provided. +Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input. + +The options are:: + + -m, --use-mnps Retain MNPs as separate events (default: false). + -t, --tag-parsed FLAG Tag records which are split apart of a complex allele with this flag. + -L, --max-length LEN Do not manipulate records in which either the ALT or + REF is longer than LEN (default: 200). + -k, --keep-info Maintain site and allele-level annotations when decomposing. + Note that in many cases, such as multisample VCFs, these won't + be valid post-decomposition. For biallelic loci in single-sample + VCFs, they should be usable with caution. + -g, --keep-geno Maintain genotype-level annotations when decomposing. Similar + caution should be used for this as for --keep-info. + +---- + +Vcfallelicprimitives @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfannotate/.shed.yml b/tool_collections/vcflib/vcfannotate/.shed.yml new file mode 100644 index 00000000000..40c3537e71b --- /dev/null +++ b/tool_collections/vcflib/vcfannotate/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: Intersect VCF records with BED annotations +homepage_url: https://github.com/ekg/vcflib +long_description: | + Intersects the records in the VCF file with targets provided in + a BED file. Intersections are done on the reference sequences in the VCF file. +name: vcfannotate +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate +type: unrestricted diff --git a/tool_collections/vcflib/vcfannotate/macros.xml b/tool_collections/vcflib/vcfannotate/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfannotate/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfannotate/test-data/vcfannotate-test1.vcf b/tool_collections/vcflib/vcfannotate/test-data/vcfannotate-test1.vcf new file mode 100644 index 00000000000..91655f5a2c1 --- /dev/null +++ b/tool_collections/vcflib/vcfannotate/test-data/vcfannotate-test1.vcf @@ -0,0 +1,32 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfannotate/test-data/vcfannotate.bed b/tool_collections/vcflib/vcfannotate/test-data/vcfannotate.bed new file mode 100644 index 00000000000..aa9c41604bf --- /dev/null +++ b/tool_collections/vcflib/vcfannotate/test-data/vcfannotate.bed @@ -0,0 +1,46 @@ +20 123251 126392 uc002wcx.3 0 + 123269 126333 0 2 76,337, 0,2804, +20 138110 139804 uc002wcy.2 0 + 138185 139665 0 2 124,390, 0,1304, +20 168526 170264 uc002wcz.1 0 - 168526 170264 0 2 233,49, 0,1689, +20 207898 210527 uc002wda.3 0 + 207929 210412 0 2 89,609, 0,2020, +20 238376 241736 uc002wdb.3 0 + 238419 239947 0 2 101,2019, 0,1341, +20 251503 271419 uc021vzl.1 0 - 251847 271244 0 11 405,119,87,102,158,100,159,119,118,49,192, 0,5105,5930,6181,6363,7467,8309,13100,18696,19396,19724, +20 251503 271419 uc002wde.2 0 - 251847 271251 0 11 405,119,87,102,158,100,159,119,118,49,188, 0,5105,5930,6181,6363,7467,8309,13100,18696,19396,19728, +20 251503 271419 uc010zpi.2 0 - 251847 270227 0 10 405,119,87,102,158,100,159,119,118,188, 0,5105,5930,6181,6363,7467,8309,13100,18696,19728, +20 256608 271079 uc010zpj.1 0 - 257400 270981 0 7 912,102,158,100,159,119,180, 0,1076,1258,2362,3204,7995,14291, +20 256608 271419 uc010zpk.2 0 - 257400 271232 0 7 912,102,158,100,159,119,188, 0,1076,1258,2362,3204,7995,14623, +20 278203 280963 uc002wdf.3 0 + 278227 279442 0 1 2760, 0, +20 306214 310872 uc002wdh.4 0 + 306568 307516 0 1 4658, 0, +20 327369 335512 uc002wdi.4 0 + 330287 334279 0 4 417,115,195,1659, 0,2523,2912,6484, +20 361307 378203 uc002wdm.3 0 + 368654 377334 0 4 506,291,293,1362, 0,7347,10623,15534, +20 361940 378203 uc002wdn.3 0 + 363189 377334 0 5 204,194,291,293,1362, 0,1136,6714,9990,14901, +20 388708 391408 uc002wdo.3 0 + 388708 388708 0 3 715,145,353, 0,1816,2347, +20 388708 400504 uc010zpl.1 0 + 389401 400429 0 6 715,145,94,199,122,303, 0,1816,9461,9667,11282,11493, +20 388708 409233 uc010zpm.1 0 + 388708 388708 0 9 715,145,94,199,122,174,112,180,99, 0,1816,9461,9667,11282,11493,14062,19248,20426, +20 388708 411610 uc002wdp.4 0 + 389401 411074 0 12 715,145,94,199,122,174,161,112,180,99,144,617, 0,1816,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc002wdq.4 0 + 389382 411074 0 11 715,94,199,122,174,161,112,180,99,144,617, 0,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc010fzy.3 0 + 388708 388708 0 12 715,145,94,199,122,174,136,112,180,99,144,617, 0,1816,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc002wdr.4 0 + 398463 411074 0 10 715,94,199,122,174,112,180,99,144,617, 0,9461,9667,11282,11493,14062,19248,20426,20886,22285, +20 416123 443187 uc002wds.3 0 - 419229 443049 0 8 3362,188,142,102,187,81,186,208, 0,3628,4768,6108,6377,9570,12409,26856, +20 416123 443187 uc002wdt.3 0 - 416123 416123 0 10 491,159,292,188,142,102,187,81,186,208, 0,1960,3070,3628,4768,6108,6377,9570,12409,26856, +20 416123 443187 uc002wdv.3 0 - 419229 422326 0 7 3362,188,142,456,81,186,208, 0,3628,4768,6108,9570,12409,26856, +20 416125 417600 uc021vzm.1 0 - 416125 416125 0 1 1475, 0, +20 463337 524482 uc002wdw.1 0 - 464604 489195 0 14 1383,87,149,101,102,111,84,60,51,102,112,210,117,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,25757,45239,60978, +20 463337 524482 uc002wdx.1 0 - 464604 489195 0 13 1383,87,149,101,102,111,84,60,51,102,112,210,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,25757,60978, +20 463337 524482 uc002wdy.1 0 - 464604 478382 0 12 1383,87,149,101,102,111,84,60,51,102,112,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,60978, +20 584636 590910 uc002wdz.3 0 - 585234 590881 0 2 673,554, 0,5720, +20 627267 634014 uc002wea.4 0 - 629357 633829 0 2 2294,395, 0,6352, +20 627267 656823 uc002web.4 0 - 629499 656245 0 3 2294,90,711, 0,7607,28845, +20 642239 656823 uc002wec.3 0 - 644314 656245 0 2 2866,711, 0,13873, +20 740723 749228 uc002wed.4 0 - 741669 746418 0 5 1159,124,506,618,288, 0,1621,3418,5128,8217, +20 740724 749228 uc002wee.2 0 - 742293 746418 0 4 1744,506,618,288, 0,3417,5127,8216, +20 814355 826922 uc002wef.1 0 + 825447 826335 0 2 239,1572, 0,10995, +20 816710 826922 uc002weg.1 0 + 825447 826335 0 2 47,1572, 0,8640, +20 825284 826922 uc002weh.1 0 + 825447 826335 0 1 1638, 0, +20 853296 896960 uc002wei.3 0 - 853602 896857 0 9 467,131,167,102,116,248,122,156,412, 0,1630,5507,7093,8517,12424,15664,17559,43252, +20 853296 896960 uc010zpn.2 0 - 853750 896839 0 8 467,167,102,116,248,122,156,412, 0,5507,7093,8517,12424,15664,17559,43252, +20 939095 982907 uc002wej.3 0 - 940999 982807 0 5 2014,186,141,189,179, 0,5482,8721,9497,43633, +20 939095 982907 uc002wek.3 0 - 940999 982807 0 4 2014,141,189,179, 0,8721,9497,43633, +20 1093905 1147970 uc010zpo.2 0 + 1106275 1146898 0 7 147,153,83,186,54,159,1100, 0,12235,14163,21858,49868,51056,52965, +20 1093905 1148426 uc002wel.4 0 + 1099416 1145724 0 8 147,150,153,83,186,54,159,2754, 0,5490,12235,14163,21858,49868,51056,51767, +20 1099239 1147970 uc010zpp.2 0 + 1099416 1146898 0 6 306,153,83,54,159,1100, 0,6901,8829,44534,45722,47631, +20 1099239 1148426 uc002wen.4 0 + 1099416 1145724 0 7 306,153,83,186,54,159,2754, 0,6901,8829,16524,44534,45722,46433, diff --git a/tool_collections/vcflib/vcfannotate/test-data/vcflib.vcf b/tool_collections/vcflib/vcfannotate/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfannotate/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfannotate/vcfannotate.xml b/tool_collections/vcflib/vcfannotate/vcfannotate.xml new file mode 100644 index 00000000000..f1876f42e1a --- /dev/null +++ b/tool_collections/vcflib/vcfannotate/vcfannotate.xml @@ -0,0 +1,51 @@ + + Intersect VCF records with BED annotations + + macros.xml + + + + vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}" + + + + + + + + + + + + + + + + + + +Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. + +----- + +.. class:: infomark + + +**Example**: + +The following VCF line:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 + 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. + +will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 + 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. + +---- + +Vcfannotate @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfannotategenotypes/.shed.yml b/tool_collections/vcflib/vcfannotategenotypes/.shed.yml new file mode 100644 index 00000000000..77ef90bd9d0 --- /dev/null +++ b/tool_collections/vcflib/vcfannotategenotypes/.shed.yml @@ -0,0 +1,13 @@ +categories: +- Variant Analysis +description: 'Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.' +homepage_url: https://github.com/ekg/vcflib +long_description: | + Annotates genotypes in the first file with genotypes in the second + adding the genotype as another flag to each sample filed in the first file. Annotation-tag + is the name of the sample flag which is added to store the annotation. also adds + a ''has\_variant'' flag for sites where the second file has a variant. +name: vcfannotategenotypes +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes +type: unrestricted diff --git a/tool_collections/vcflib/vcfannotategenotypes/macros.xml b/tool_collections/vcflib/vcfannotategenotypes/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfannotategenotypes/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfannotategenotypes/test-data/vcfannotategenotypes-input2.vcf b/tool_collections/vcflib/vcfannotategenotypes/test-data/vcfannotategenotypes-input2.vcf new file mode 100644 index 00000000000..ebfcec99b4b --- /dev/null +++ b/tool_collections/vcflib/vcfannotategenotypes/test-data/vcfannotategenotypes-input2.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 . +X 10 rsTest AC A,ATG 10 PASS . GT 0 0|2 diff --git a/tool_collections/vcflib/vcfannotategenotypes/test-data/vcfannotategenotypes-test1.vcf b/tool_collections/vcflib/vcfannotategenotypes/test-data/vcfannotategenotypes-test1.vcf new file mode 100644 index 00000000000..f867da394e7 --- /dev/null +++ b/tool_collections/vcflib/vcfannotategenotypes/test-data/vcfannotategenotypes-test1.vcf @@ -0,0 +1,33 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 +19 112 . A G 10 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:48:1:51,51:0/0 1|0:48:8:51,51:./. 1/1:43:5:.,.:1/1 +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:49:3:58,50:0/0 0|1:3:5:65,3:./. 0/0:41:3:.,.:0/0 +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1/2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2 +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0/0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0 +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant GT:GQ:DP:added-genotypes 0/1:.:4:0/1 0/2:17:2:./. 1/1:40:3:1/1 +20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:. +X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0/2 diff --git a/tool_collections/vcflib/vcfannotategenotypes/test-data/vcflib.vcf b/tool_collections/vcflib/vcfannotategenotypes/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfannotategenotypes/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfannotategenotypes/vcfannotategenotypes.xml b/tool_collections/vcflib/vcfannotategenotypes/vcfannotategenotypes.xml new file mode 100644 index 00000000000..b9a363d5b89 --- /dev/null +++ b/tool_collections/vcflib/vcfannotategenotypes/vcfannotategenotypes.xml @@ -0,0 +1,34 @@ + + Annotate genotypes in a VCF dataset using genotypes from another VCF dataset + + macros.xml + + + + vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}" + + + + + + + + + + + + + + + + + + +Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation. Also adds a 'has\_variant' flag for sites where the second file has a variant. + +----- + +Vcfannotate @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfbedintersect/.shed.yml b/tool_collections/vcflib/vcfbedintersect/.shed.yml new file mode 100644 index 00000000000..949f49cb03b --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Variant Analysis +description: Intersect VCF and BED datasets +homepage_url: https://github.com/ekg/vcflib +long_description: | + Computes intersection between a VCF dataset and a set of genomic + intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) + or a manually typed interval (in the form of chr:start-end). +name: vcfbedintersect +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect +type: unrestricted diff --git a/tool_collections/vcflib/vcfbedintersect/macros.xml b/tool_collections/vcflib/vcfbedintersect/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfbedintersect/test-data/vcfannotate.bed b/tool_collections/vcflib/vcfbedintersect/test-data/vcfannotate.bed new file mode 100644 index 00000000000..aa9c41604bf --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/test-data/vcfannotate.bed @@ -0,0 +1,46 @@ +20 123251 126392 uc002wcx.3 0 + 123269 126333 0 2 76,337, 0,2804, +20 138110 139804 uc002wcy.2 0 + 138185 139665 0 2 124,390, 0,1304, +20 168526 170264 uc002wcz.1 0 - 168526 170264 0 2 233,49, 0,1689, +20 207898 210527 uc002wda.3 0 + 207929 210412 0 2 89,609, 0,2020, +20 238376 241736 uc002wdb.3 0 + 238419 239947 0 2 101,2019, 0,1341, +20 251503 271419 uc021vzl.1 0 - 251847 271244 0 11 405,119,87,102,158,100,159,119,118,49,192, 0,5105,5930,6181,6363,7467,8309,13100,18696,19396,19724, +20 251503 271419 uc002wde.2 0 - 251847 271251 0 11 405,119,87,102,158,100,159,119,118,49,188, 0,5105,5930,6181,6363,7467,8309,13100,18696,19396,19728, +20 251503 271419 uc010zpi.2 0 - 251847 270227 0 10 405,119,87,102,158,100,159,119,118,188, 0,5105,5930,6181,6363,7467,8309,13100,18696,19728, +20 256608 271079 uc010zpj.1 0 - 257400 270981 0 7 912,102,158,100,159,119,180, 0,1076,1258,2362,3204,7995,14291, +20 256608 271419 uc010zpk.2 0 - 257400 271232 0 7 912,102,158,100,159,119,188, 0,1076,1258,2362,3204,7995,14623, +20 278203 280963 uc002wdf.3 0 + 278227 279442 0 1 2760, 0, +20 306214 310872 uc002wdh.4 0 + 306568 307516 0 1 4658, 0, +20 327369 335512 uc002wdi.4 0 + 330287 334279 0 4 417,115,195,1659, 0,2523,2912,6484, +20 361307 378203 uc002wdm.3 0 + 368654 377334 0 4 506,291,293,1362, 0,7347,10623,15534, +20 361940 378203 uc002wdn.3 0 + 363189 377334 0 5 204,194,291,293,1362, 0,1136,6714,9990,14901, +20 388708 391408 uc002wdo.3 0 + 388708 388708 0 3 715,145,353, 0,1816,2347, +20 388708 400504 uc010zpl.1 0 + 389401 400429 0 6 715,145,94,199,122,303, 0,1816,9461,9667,11282,11493, +20 388708 409233 uc010zpm.1 0 + 388708 388708 0 9 715,145,94,199,122,174,112,180,99, 0,1816,9461,9667,11282,11493,14062,19248,20426, +20 388708 411610 uc002wdp.4 0 + 389401 411074 0 12 715,145,94,199,122,174,161,112,180,99,144,617, 0,1816,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc002wdq.4 0 + 389382 411074 0 11 715,94,199,122,174,161,112,180,99,144,617, 0,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc010fzy.3 0 + 388708 388708 0 12 715,145,94,199,122,174,136,112,180,99,144,617, 0,1816,9461,9667,11282,11493,12806,14062,19248,20426,20886,22285, +20 388708 411610 uc002wdr.4 0 + 398463 411074 0 10 715,94,199,122,174,112,180,99,144,617, 0,9461,9667,11282,11493,14062,19248,20426,20886,22285, +20 416123 443187 uc002wds.3 0 - 419229 443049 0 8 3362,188,142,102,187,81,186,208, 0,3628,4768,6108,6377,9570,12409,26856, +20 416123 443187 uc002wdt.3 0 - 416123 416123 0 10 491,159,292,188,142,102,187,81,186,208, 0,1960,3070,3628,4768,6108,6377,9570,12409,26856, +20 416123 443187 uc002wdv.3 0 - 419229 422326 0 7 3362,188,142,456,81,186,208, 0,3628,4768,6108,9570,12409,26856, +20 416125 417600 uc021vzm.1 0 - 416125 416125 0 1 1475, 0, +20 463337 524482 uc002wdw.1 0 - 464604 489195 0 14 1383,87,149,101,102,111,84,60,51,102,112,210,117,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,25757,45239,60978, +20 463337 524482 uc002wdx.1 0 - 464604 489195 0 13 1383,87,149,101,102,111,84,60,51,102,112,210,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,25757,60978, +20 463337 524482 uc002wdy.1 0 - 464604 478382 0 12 1383,87,149,101,102,111,84,60,51,102,112,167, 0,3682,4733,5984,7086,9560,13025,15027,16561,17139,22424,60978, +20 584636 590910 uc002wdz.3 0 - 585234 590881 0 2 673,554, 0,5720, +20 627267 634014 uc002wea.4 0 - 629357 633829 0 2 2294,395, 0,6352, +20 627267 656823 uc002web.4 0 - 629499 656245 0 3 2294,90,711, 0,7607,28845, +20 642239 656823 uc002wec.3 0 - 644314 656245 0 2 2866,711, 0,13873, +20 740723 749228 uc002wed.4 0 - 741669 746418 0 5 1159,124,506,618,288, 0,1621,3418,5128,8217, +20 740724 749228 uc002wee.2 0 - 742293 746418 0 4 1744,506,618,288, 0,3417,5127,8216, +20 814355 826922 uc002wef.1 0 + 825447 826335 0 2 239,1572, 0,10995, +20 816710 826922 uc002weg.1 0 + 825447 826335 0 2 47,1572, 0,8640, +20 825284 826922 uc002weh.1 0 + 825447 826335 0 1 1638, 0, +20 853296 896960 uc002wei.3 0 - 853602 896857 0 9 467,131,167,102,116,248,122,156,412, 0,1630,5507,7093,8517,12424,15664,17559,43252, +20 853296 896960 uc010zpn.2 0 - 853750 896839 0 8 467,167,102,116,248,122,156,412, 0,5507,7093,8517,12424,15664,17559,43252, +20 939095 982907 uc002wej.3 0 - 940999 982807 0 5 2014,186,141,189,179, 0,5482,8721,9497,43633, +20 939095 982907 uc002wek.3 0 - 940999 982807 0 4 2014,141,189,179, 0,8721,9497,43633, +20 1093905 1147970 uc010zpo.2 0 + 1106275 1146898 0 7 147,153,83,186,54,159,1100, 0,12235,14163,21858,49868,51056,52965, +20 1093905 1148426 uc002wel.4 0 + 1099416 1145724 0 8 147,150,153,83,186,54,159,2754, 0,5490,12235,14163,21858,49868,51056,51767, +20 1099239 1147970 uc010zpp.2 0 + 1099416 1146898 0 6 306,153,83,54,159,1100, 0,6901,8829,44534,45722,47631, +20 1099239 1148426 uc002wen.4 0 + 1099416 1145724 0 7 306,153,83,186,54,159,2754, 0,6901,8829,16524,44534,45722,46433, diff --git a/tool_collections/vcflib/vcfbedintersect/test-data/vcfbedintersect-test1.vcf b/tool_collections/vcflib/vcfbedintersect/test-data/vcfbedintersect-test1.vcf new file mode 100644 index 00000000000..78d89f7d1be --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/test-data/vcfbedintersect-test1.vcf @@ -0,0 +1,23 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. diff --git a/tool_collections/vcflib/vcfbedintersect/test-data/vcfbedintersect-test2.vcf b/tool_collections/vcflib/vcfbedintersect/test-data/vcfbedintersect-test2.vcf new file mode 100644 index 00000000000..06c9cd65726 --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/test-data/vcfbedintersect-test2.vcf @@ -0,0 +1,24 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. diff --git a/tool_collections/vcflib/vcfbedintersect/test-data/vcflib.vcf b/tool_collections/vcflib/vcfbedintersect/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfbedintersect/vcfbedintersect.xml b/tool_collections/vcflib/vcfbedintersect/vcfbedintersect.xml new file mode 100644 index 00000000000..0530de37eb9 --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/vcfbedintersect.xml @@ -0,0 +1,59 @@ + + Intersect VCF and BED datasets + + macros.xml + + + + + #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": + vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}" + #else: + vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end). + +---- + +VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + + diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/.shed.yml b/tool_collections/vcflib/vcfbreakcreatemulti/.shed.yml new file mode 100644 index 00000000000..7ff96c09291 --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/.shed.yml @@ -0,0 +1,17 @@ +categories: +- Variant Analysis +description: Break multiple alleles into multiple records, or combine overallpoing + alleles into a single record +homepage_url: https://github.com/ekg/vcflib +long_description: | + This tool breaks or creates multiallelic VCF records based on user + selection. + + - Breaking = If multiple alleles are specified in a single record, break the record + into multiple lines, preserving allele-specific INFO fields. + - Creation = If overlapping alleles are represented across multiple records, merge + them into a single record. +name: vcfbreakcreatemulti +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti +type: unrestricted diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/macros.xml b/tool_collections/vcflib/vcfbreakcreatemulti/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test1.vcf b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test1.vcf new file mode 100644 index 00000000000..9c4104947be --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test1.vcf @@ -0,0 +1,34 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . 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GT 0 ./0 0|1 diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test2-input.vcf b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test2-input.vcf new file mode 100644 index 00000000000..acc549c6e0d --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test2-input.vcf @@ -0,0 +1,34 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . 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GT 0 ./0 0/1 diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test2.vcf b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test2.vcf new file mode 100644 index 00000000000..c98893f361c --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcfbreakcreatemulti-test2.vcf @@ -0,0 +1,32 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;combined=1110696-1110696;DB GT:GQ:DP:HQ ./1:21:6:23,27 ./1:2:0:18,2 ./.:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;combined=1234567-1234567 GT:GQ:DP 0/1:.:4 ./0:17:2 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 0|0 . +X 10 rsTest AC A,ATG 10 PASS combined=10-10 GT 0 0/1 ./0 diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcflib.vcf b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfbreakcreatemulti/vcfbreakcreatemulti.xml b/tool_collections/vcflib/vcfbreakcreatemulti/vcfbreakcreatemulti.xml new file mode 100644 index 00000000000..58eaf85afcb --- /dev/null +++ b/tool_collections/vcflib/vcfbreakcreatemulti/vcfbreakcreatemulti.xml @@ -0,0 +1,48 @@ + + Break multiple alleles into multiple records, or combine overallpoing alleles into a single record + + macros.xml + + + + + #if str($break_or_create) == "break": + vcfbreakmulti "${input1}" > "${out_file1}" + #elif str($break_or_create) == "create": + vcfcreatemulti "${input1}" > "${out_file1}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + +This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): + + - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. + - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. + +---- + +This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + + diff --git a/tool_collections/vcflib/vcfcheck/.shed.yml b/tool_collections/vcflib/vcfcheck/.shed.yml new file mode 100644 index 00000000000..efe75c86012 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Variant Analysis +description: Verify that the reference allele matches the reference genome +homepage_url: https://github.com/ekg/vcflib +long_description: | + Verifies that the VCF REF field matches the reference as described +name: vcfcheck +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck +type: unrestricted diff --git a/tool_collections/vcflib/vcfcheck/macros.xml b/tool_collections/vcflib/vcfcheck/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfcheck/test-data/vcfcheck-test1.vcf b/tool_collections/vcflib/vcfcheck/test-data/vcfcheck-test1.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/test-data/vcfcheck-test1.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfcheck/test-data/vcflib-phix.vcf b/tool_collections/vcflib/vcfcheck/test-data/vcflib-phix.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/test-data/vcflib-phix.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfcheck/test-data/vcflib-test-genome-phix.fa b/tool_collections/vcflib/vcfcheck/test-data/vcflib-test-genome-phix.fa new file mode 100644 index 00000000000..48a6b46678a --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/test-data/vcflib-test-genome-phix.fa @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff --git a/tool_collections/vcflib/vcfcheck/tool-data/fasta_indexes.loc.sample b/tool_collections/vcflib/vcfcheck/tool-data/fasta_indexes.loc.sample new file mode 120000 index 00000000000..6d7aec6c449 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/tool-data/fasta_indexes.loc.sample @@ -0,0 +1 @@ +../../tool-data/fasta_indexes.loc.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfcheck/tool-data/tool_data_table_conf.xml.sample b/tool_collections/vcflib/vcfcheck/tool-data/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..7bfcf015ca6 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/tool-data/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../../tool-data/tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfcheck/vcfcheck.xml b/tool_collections/vcflib/vcfcheck/vcfcheck.xml new file mode 100644 index 00000000000..7f78e5ec741 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/vcfcheck.xml @@ -0,0 +1,74 @@ + + Verify that the reference allele matches the reference genome + + macros.xml + + + + + + + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Verifies that the VCF REF field matches the reference as described. + +The options are:: + + -x, --exclude-failures If a record fails, don't print it. Otherwise do. + -k, --keep-failures Print if the record fails, otherwise not. + +---- + +Vcfcheck @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfcombine/.shed.yml b/tool_collections/vcflib/vcfcombine/.shed.yml new file mode 100644 index 00000000000..e7996d61b67 --- /dev/null +++ b/tool_collections/vcflib/vcfcombine/.shed.yml @@ -0,0 +1,14 @@ +categories: +- Variant Analysis +description: Combine multiple VCF datasets +homepage_url: https://github.com/ekg/vcflib +long_description: | + Combines VCF files positionally, combining samples when sites and + alleles are identical. Any number of VCF files may be combined. The INFO field and + other columns are taken from one of the files which are combined when records in + multiple files match. Alleles must have identical ordering to be combined into one + record. If they do not, multiple records will be emitted. +name: vcfcombine +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine +type: unrestricted diff --git a/tool_collections/vcflib/vcfcombine/macros.xml b/tool_collections/vcflib/vcfcombine/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfcombine/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfcombine/test-data/vcfcombine-test1.vcf b/tool_collections/vcflib/vcfcombine/test-data/vcfcombine-test1.vcf new file mode 100644 index 00000000000..31d09fb21b5 --- /dev/null +++ b/tool_collections/vcflib/vcfcombine/test-data/vcfcombine-test1.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2 GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfcombine/test-data/vcflib.vcf b/tool_collections/vcflib/vcfcombine/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfcombine/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfcombine/vcfcombine.xml b/tool_collections/vcflib/vcfcombine/vcfcombine.xml new file mode 100644 index 00000000000..2a564eec975 --- /dev/null +++ b/tool_collections/vcflib/vcfcombine/vcfcombine.xml @@ -0,0 +1,39 @@ + + Combine multiple VCF datasets + + macros.xml + + + + + vcfcombine + + #for $input_vcf in $input_vcfs: + "${input_vcf}" + #end for + + > "${out_file1}" + + + + + + + + + + + + + + + + +Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted. + +----- + +Vcfcombine @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfcommonsamples/.shed.yml b/tool_collections/vcflib/vcfcommonsamples/.shed.yml new file mode 100644 index 00000000000..684327a8031 --- /dev/null +++ b/tool_collections/vcflib/vcfcommonsamples/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Variant Analysis +description: Output records belonging to samples commong between two datasets. +homepage_url: https://github.com/ekg/vcflib +long_description: | + Outputs each record in the first file, removing samples not present in the second. +name: vcfcommonsamples +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples +type: unrestricted diff --git a/tool_collections/vcflib/vcfcommonsamples/macros.xml b/tool_collections/vcflib/vcfcommonsamples/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfcommonsamples/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfcommonsamples/test-data/vcfcommonsamples-test1-input2.vcf b/tool_collections/vcflib/vcfcommonsamples/test-data/vcfcommonsamples-test1-input2.vcf new file mode 100644 index 00000000000..ebfcec99b4b --- /dev/null +++ b/tool_collections/vcflib/vcfcommonsamples/test-data/vcfcommonsamples-test1-input2.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 . +X 10 rsTest AC A,ATG 10 PASS . GT 0 0|2 diff --git a/tool_collections/vcflib/vcfcommonsamples/test-data/vcfcommonsamples-test1.vcf b/tool_collections/vcflib/vcfcommonsamples/test-data/vcfcommonsamples-test1.vcf new file mode 100644 index 00000000000..01f2a43aeaa --- /dev/null +++ b/tool_collections/vcflib/vcfcommonsamples/test-data/vcfcommonsamples-test1.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0|2 diff --git a/tool_collections/vcflib/vcfcommonsamples/test-data/vcflib.vcf b/tool_collections/vcflib/vcfcommonsamples/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfcommonsamples/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfcommonsamples/vcfcommonsamples.xml b/tool_collections/vcflib/vcfcommonsamples/vcfcommonsamples.xml new file mode 100644 index 00000000000..655c5dcb61d --- /dev/null +++ b/tool_collections/vcflib/vcfcommonsamples/vcfcommonsamples.xml @@ -0,0 +1,32 @@ + + Output records belonging to samples common between two datasets + + macros.xml + + + + vcfcommonsamples "${input1}" "${input2}" > "${out_file1}" + + + + + + + + + + + + + + + + +Outputs each record in the first file, removing samples not present in the second. + +---- + +Vcfcommonsamples @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfdistance/.shed.yml b/tool_collections/vcflib/vcfdistance/.shed.yml new file mode 100644 index 00000000000..26cc59189ea --- /dev/null +++ b/tool_collections/vcflib/vcfdistance/.shed.yml @@ -0,0 +1,14 @@ +categories: +- Variant Analysis +description: Calculate distance to the nearest variant. +homepage_url: https://github.com/ekg/vcflib +long_description: | + Adds a value to each VCF record indicating the distance to the + nearest variant in the file. The dataset used as input to this tool must be + coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy''s + general purpose sort tool (in this case sort on the first and the second column + in ascending order). +name: vcfdistance +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance +type: unrestricted diff --git a/tool_collections/vcflib/vcfdistance/macros.xml b/tool_collections/vcflib/vcfdistance/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfdistance/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfdistance/test-data/vcfdistance-test1.vcf b/tool_collections/vcflib/vcfdistance/test-data/vcfdistance-test1.vcf new file mode 100644 index 00000000000..007aaac14be --- /dev/null +++ b/tool_collections/vcflib/vcfdistance/test-data/vcfdistance-test1.vcf @@ -0,0 +1,32 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;BasesToClosestVariant=2960;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;BasesToClosestVariant=2960;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BasesToClosestVariant=119541;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;BasesToClosestVariant=4330;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;BasesToClosestVariant=670;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . 0 . BasesToClosestVariant=670 GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfdistance/test-data/vcflib.vcf b/tool_collections/vcflib/vcfdistance/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfdistance/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfdistance/vcfdistance.xml b/tool_collections/vcflib/vcfdistance/vcfdistance.xml new file mode 100644 index 00000000000..baf5b72304c --- /dev/null +++ b/tool_collections/vcflib/vcfdistance/vcfdistance.xml @@ -0,0 +1,34 @@ + + Calculate distance to the nearest variant + + macros.xml + + + + cat "${input1}" | vcfdistance > "${out_file1}" + + + + + + + + + + + + + + +Adds a value to each VCF record indicating the distance to the nearest variant in the file. + +.. class:: infomark + +The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). + +---- + +Vcfdistance @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcffilter/.shed.yml b/tool_collections/vcflib/vcffilter/.shed.yml new file mode 100644 index 00000000000..48519581713 --- /dev/null +++ b/tool_collections/vcflib/vcffilter/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: Tool for filtering VCF files +homepage_url: https://github.com/ekg/vcflib +long_description: | + A vcflib-based tool for flexible filtering of VCF datasets on a + variety of tags. This is a galaxy wrapper for vcffilter utility from vcflib package. +name: vcffilter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter +type: unrestricted diff --git a/tool_collections/vcflib/vcffilter/macros.xml b/tool_collections/vcflib/vcffilter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcffilter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcffilter/test-data/vcffilter-test1.vcf b/tool_collections/vcflib/vcffilter/test-data/vcffilter-test1.vcf new file mode 100644 index 00000000000..fa6d831c5d6 --- /dev/null +++ b/tool_collections/vcflib/vcffilter/test-data/vcffilter-test1.vcf @@ -0,0 +1,26 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##filter="DP > 10" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. diff --git a/tool_collections/vcflib/vcffilter/test-data/vcflib.vcf b/tool_collections/vcflib/vcffilter/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcffilter/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcffilter/vcffilter.xml b/tool_collections/vcflib/vcffilter/vcffilter.xml new file mode 100644 index 00000000000..a0f19c22475 --- /dev/null +++ b/tool_collections/vcflib/vcffilter/vcffilter.xml @@ -0,0 +1,76 @@ + + filter VCF data in a variety of attributes + + macros.xml + + + htslib + + + + + ln -s "${input1}" input1.vcf && + bgzip input1.vcf && + tabix -p vcf input1.vcf.gz && + vcffilter ${filterList} input1.vcf.gz > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + +You can specify the following options within the **Specify filtering expression** box in any combination:: + + -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter + -g, --genotype-filter specifies a filter to apply to the genotype fields of records + -s, --filter-sites filter entire records, not just alleles + -t, --tag-pass tag vcf records as positively filtered with this tag, print all records + -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records + -A, --append-filter append the existing filter tag, don't just replace it + -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag + -v, --invert inverts the filter, e.g. grep -v + -o, --or use logical OR instead of AND to combine filters + -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g) + +Filters are specified in the form {ID} {operator} {value}:: + + -f "DP > 10" # for info fields + -g "GT = 1|1" # for genotype fields + -f "CpG" # for 'flag' fields + +Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields. + +Operators can be any of: =, !, <, >, pipe, & + + +To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: + + -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 + -r chrX # only output call on chromosome X + +----- + +Vcffilter @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcffixup/.shed.yml b/tool_collections/vcflib/vcffixup/.shed.yml new file mode 100644 index 00000000000..97c7932d4a5 --- /dev/null +++ b/tool_collections/vcflib/vcffixup/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: 'Count the allele frequencies across alleles present in each record in the VCF file.' +homepage_url: https://github.com/ekg/vcflib +long_description: | + Uses genotypes from the VCF file to correct AC (alternate allele + count), AF (alternate allele frequency), NS (number of called), in the VCF records. +name: vcffixup +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup +type: unrestricted diff --git a/tool_collections/vcflib/vcffixup/macros.xml b/tool_collections/vcflib/vcffixup/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcffixup/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcffixup/test-data/vcffixup-test1.vcf b/tool_collections/vcflib/vcffixup/test-data/vcffixup-test1.vcf new file mode 100644 index 00000000000..8f76832065a --- /dev/null +++ b/tool_collections/vcflib/vcffixup/test-data/vcffixup-test1.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . AC=1;AF=0.166667;AN=6;NS=3 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . AC=1;AF=0.166667;AN=6;NS=3 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AC=3;AF=0.5;AN=6;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AC=1;AF=0.166667;AN=6;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AC=2,4;AF=0.333333,0.666667;AN=6;DP=10;NS=3;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;AC=0;AF=0;AN=6;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AF=0.5,0.166667;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . 0 . AC=0;AF=0;AN=4;NS=3 GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS AC=1,1;AF=0.2,0.2;AN=5;NS=3 GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcffixup/test-data/vcflib.vcf b/tool_collections/vcflib/vcffixup/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcffixup/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcffixup/vcffixup.xml b/tool_collections/vcflib/vcffixup/vcffixup.xml new file mode 100644 index 00000000000..754510c59b8 --- /dev/null +++ b/tool_collections/vcflib/vcffixup/vcffixup.xml @@ -0,0 +1,30 @@ + + Count the allele frequencies across alleles present in each record in the VCF file + + macros.xml + + + + vcffixup "${input1}" > "${out_file1}" + + + + + + + + + + + + + + +Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records. + +---- + +Vcffixup @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfflatten/.shed.yml b/tool_collections/vcflib/vcfflatten/.shed.yml new file mode 100644 index 00000000000..07c679e69f2 --- /dev/null +++ b/tool_collections/vcflib/vcfflatten/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Variant Analysis +description: Removes multi-allelic sites by picking the most common alternate +homepage_url: https://github.com/ekg/vcflib +long_description: | + Removes multi-allelic sites by picking the most common alternate. + Requires allele frequency specification ''AF'' and use of ''G'' and ''A'' to specify + the fields which vary according to the Allele or Genotype. +name: vcfflatten +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten +type: unrestricted diff --git a/tool_collections/vcflib/vcfflatten/macros.xml b/tool_collections/vcflib/vcfflatten/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfflatten/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfflatten/test-data/vcfflatten-input1.vcf b/tool_collections/vcflib/vcfflatten/test-data/vcfflatten-input1.vcf new file mode 100644 index 00000000000..ff8bfd3b023 --- /dev/null +++ b/tool_collections/vcflib/vcfflatten/test-data/vcfflatten-input1.vcf @@ -0,0 +1,121 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, diff --git a/tool_collections/vcflib/vcfflatten/test-data/vcfflatten-test1.vcf b/tool_collections/vcflib/vcfflatten/test-data/vcfflatten-test1.vcf new file mode 100644 index 00000000000..8b4fdcbc451 --- /dev/null +++ b/tool_collections/vcflib/vcfflatten/test-data/vcfflatten-test1.vcf @@ -0,0 +1,121 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G 0 . AC=3;AF=0.038961038961 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, diff --git a/tool_collections/vcflib/vcfflatten/vcfflatten.xml b/tool_collections/vcflib/vcfflatten/vcfflatten.xml new file mode 100644 index 00000000000..4ac8d6d6548 --- /dev/null +++ b/tool_collections/vcflib/vcfflatten/vcfflatten.xml @@ -0,0 +1,30 @@ + + Removes multi-allelic sites by picking the most common alternate + + macros.xml + + + + vcfflatten "${input1}" > "${out_file1}" + + + + + + + + + + + + + + +Removes multi-allelic sites by picking the most common alternate. Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype. + +---- + +Vcfflatten @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfgeno2haplo/.shed.yml b/tool_collections/vcflib/vcfgeno2haplo/.shed.yml new file mode 100644 index 00000000000..761ec15e4d3 --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Variant Analysis +description: Convert genotype-based phased alleles into haplotype alleles +homepage_url: https://github.com/ekg/vcflib +long_description: | + Convert genotype-based phased alleles within a window size specified + by -w option into haplotype alleles. Will break haplotype construction when encountering + non-phased genotypes on input. +name: vcfgeno2haplo +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo +type: unrestricted diff --git a/tool_collections/vcflib/vcfgeno2haplo/macros.xml b/tool_collections/vcflib/vcfgeno2haplo/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfgeno2haplo/test-data/vcfgeno2haplo-test1.vcf b/tool_collections/vcflib/vcfgeno2haplo/test-data/vcfgeno2haplo-test1.vcf new file mode 100644 index 00000000000..64e79fd753d --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/test-data/vcfgeno2haplo-test1.vcf @@ -0,0 +1,12 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB diff --git a/tool_collections/vcflib/vcfgeno2haplo/test-data/vcflib-phix.vcf b/tool_collections/vcflib/vcfgeno2haplo/test-data/vcflib-phix.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/test-data/vcflib-phix.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfgeno2haplo/test-data/vcflib-test-genome-phix.fa b/tool_collections/vcflib/vcfgeno2haplo/test-data/vcflib-test-genome-phix.fa new file mode 100644 index 00000000000..48a6b46678a --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/test-data/vcflib-test-genome-phix.fa @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff --git a/tool_collections/vcflib/vcfgeno2haplo/tool-data/fasta_indexes.loc.sample b/tool_collections/vcflib/vcfgeno2haplo/tool-data/fasta_indexes.loc.sample new file mode 120000 index 00000000000..6d7aec6c449 --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/tool-data/fasta_indexes.loc.sample @@ -0,0 +1 @@ +../../tool-data/fasta_indexes.loc.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfgeno2haplo/tool-data/tool_data_table_conf.xml.sample b/tool_collections/vcflib/vcfgeno2haplo/tool-data/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..7bfcf015ca6 --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/tool-data/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../../tool-data/tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfgeno2haplo/vcfgeno2haplo.xml b/tool_collections/vcflib/vcfgeno2haplo/vcfgeno2haplo.xml new file mode 100644 index 00000000000..a2c2d1d8c7d --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/vcfgeno2haplo.xml @@ -0,0 +1,75 @@ + + Convert genotype-based phased alleles into haplotype alleles + + macros.xml + + + + + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input. + +The options are:: + + -w, --window-size N Merge variants at most this many bp apart (default 30) + -o, --only-variants Don't output the entire haplotype, just concatenate + REF/ALT strings (delimited by ":") + +---- + +Vcfgeno2haplo @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfgenotypes/.shed.yml b/tool_collections/vcflib/vcfgenotypes/.shed.yml new file mode 100644 index 00000000000..4125d76b784 --- /dev/null +++ b/tool_collections/vcflib/vcfgenotypes/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: Convert numerical representation of genotypes to allelic. +homepage_url: https://github.com/ekg/vcflib +long_description: | + Converts numerical representation of genotypes (standard in GT + field) to the alleles provided in the call''s ALT/REF fields. +name: vcfgenotypes +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes +type: unrestricted diff --git a/tool_collections/vcflib/vcfgenotypes/macros.xml b/tool_collections/vcflib/vcfgenotypes/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfgenotypes/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfgenotypes/test-data/vcfgenotypes-test1.tab b/tool_collections/vcflib/vcfgenotypes/test-data/vcfgenotypes-test1.tab new file mode 100644 index 00000000000..5d5b50d6064 --- /dev/null +++ b/tool_collections/vcflib/vcfgenotypes/test-data/vcfgenotypes-test1.tab @@ -0,0 +1,9 @@ +19 111 A C A,C NA00001:A/A NA00002:A/A NA00003:A/C +19 112 A G A,G NA00001:A/A NA00002:A/A NA00003:A/G +20 14370 G A G,A NA00001:G/G NA00002:A/G NA00003:A/A +20 17330 T A T,A NA00001:T/T NA00002:T/A NA00003:T/T +20 1110696 A G,T A,G,T NA00001:G/T NA00002:T/G NA00003:T/T +20 1230237 T . T,. NA00001:T/T NA00002:T/T NA00003:T/T +20 1234567 G GA,GAC G,GA,GAC NA00001:G/GA NA00002:G/GAC NA00003:GA/GA +20 1235237 T . T,. NA00001:T/T NA00002:T/T NA00003:T/T +X 10 AC A,ATG AC,A,ATG NA00001:AC NA00002:AC/A NA00003:AC/ATG diff --git a/tool_collections/vcflib/vcfgenotypes/test-data/vcflib.vcf b/tool_collections/vcflib/vcfgenotypes/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfgenotypes/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfgenotypes/vcfgenotypes.xml b/tool_collections/vcflib/vcfgenotypes/vcfgenotypes.xml new file mode 100644 index 00000000000..ccf7d476db6 --- /dev/null +++ b/tool_collections/vcflib/vcfgenotypes/vcfgenotypes.xml @@ -0,0 +1,30 @@ + + Convert numerical representation of genotypes to allelic + + macros.xml + + + + vcfgenotypes "${vcf_input}" > "${out_file1}" + + + + + + + + + + + + + + +Converts numerical representation of genotypes (standard in GT field) to the alleles provided in the call's ALT/REF fields. + +---- + +Vcfgenotypes @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfhethom/.shed.yml b/tool_collections/vcflib/vcfhethom/.shed.yml new file mode 100644 index 00000000000..0ff2bc3f4be --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/.shed.yml @@ -0,0 +1,14 @@ +categories: +- Variant Analysis +description: 'Count the number of heterozygotes and alleles, compute het/hom ratio.' +homepage_url: https://github.com/ekg/vcflib +long_description: | + This tool perfoms three basic calculations: + + (1) Computes the number of heterozygotes + (2) Computes the ratio between heterozygotes and homozygotes + (3) Computes the total number of alleles in the input dataset +name: vcfhethom +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom +type: unrestricted diff --git a/tool_collections/vcflib/vcfhethom/macros.xml b/tool_collections/vcflib/vcfhethom/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test1.tab b/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test1.tab new file mode 100644 index 00000000000..bc3c3b9c672 --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test1.tab @@ -0,0 +1,2 @@ +NA00001 NA00002 NA00003 +1 4 3 diff --git a/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test2.tab b/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test2.tab new file mode 100644 index 00000000000..307bec64b2b --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test2.tab @@ -0,0 +1,2 @@ +NA00001 NA00002 NA00003 +inf inf 0.75 diff --git a/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test3.tab b/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test3.tab new file mode 100644 index 00000000000..aabe6ec3909 --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/test-data/vcfhethom-test3.tab @@ -0,0 +1 @@ +21 diff --git a/tool_collections/vcflib/vcfhethom/test-data/vcflib.vcf b/tool_collections/vcflib/vcfhethom/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfhethom/vcfhethom.xml b/tool_collections/vcflib/vcfhethom/vcfhethom.xml new file mode 100644 index 00000000000..60cce1b877d --- /dev/null +++ b/tool_collections/vcflib/vcfhethom/vcfhethom.xml @@ -0,0 +1,61 @@ + + Count the number of heterozygotes and alleles, compute het/hom ratio + + macros.xml + + + + + + #if str($analysis_type) == "count": + vcfhetcount "${vcf_input}" > "${out_file1}" + #elif str($analysis_type) == "ratio": + vcfhethomratio "${vcf_input}" > "${out_file1}" + #elif str($analysis_type) == "allele_count": + vcfcountalleles "${vcf_input}" > "${out_file1}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool performs three basic calculations: + +(1) Computes the number of heterozygotes +(2) Computes the ratio between heterozygotes and homozygotes +(3) Computes the total number of alleles in the input dataset + +---- + +This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + + + diff --git a/tool_collections/vcflib/vcfleftalign/.shed.yml b/tool_collections/vcflib/vcfleftalign/.shed.yml new file mode 100644 index 00000000000..6f9db4f6775 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Variant Analysis +description: Left-align indels and complex variants in VCF dataset +homepage_url: https://github.com/ekg/vcflib +long_description: | + Left-aligns variants in VCF dataset. Window size is determined + dynamically according to the entropy of the regions flanking the indel. These must + have entropy > 1 bit/bp, or be shorter than ~5kb. +name: vcfleftalign +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign +type: unrestricted diff --git a/tool_collections/vcflib/vcfleftalign/macros.xml b/tool_collections/vcflib/vcfleftalign/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfleftalign/test-data/vcfleftalign-test1.vcf b/tool_collections/vcflib/vcfleftalign/test-data/vcfleftalign-test1.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/test-data/vcfleftalign-test1.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfleftalign/test-data/vcflib-phix.vcf b/tool_collections/vcflib/vcfleftalign/test-data/vcflib-phix.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/test-data/vcflib-phix.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfleftalign/test-data/vcflib-test-genome-phix.fa b/tool_collections/vcflib/vcfleftalign/test-data/vcflib-test-genome-phix.fa new file mode 100644 index 00000000000..48a6b46678a --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/test-data/vcflib-test-genome-phix.fa @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff --git a/tool_collections/vcflib/vcfleftalign/tool-data/fasta_indexes.loc.sample b/tool_collections/vcflib/vcfleftalign/tool-data/fasta_indexes.loc.sample new file mode 120000 index 00000000000..6d7aec6c449 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/tool-data/fasta_indexes.loc.sample @@ -0,0 +1 @@ +../../tool-data/fasta_indexes.loc.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfleftalign/tool-data/tool_data_table_conf.xml.sample b/tool_collections/vcflib/vcfleftalign/tool-data/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..7bfcf015ca6 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/tool-data/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../../tool-data/tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfleftalign/vcfleftalign.xml b/tool_collections/vcflib/vcfleftalign/vcfleftalign.xml new file mode 100644 index 00000000000..c3f968d987f --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/vcfleftalign.xml @@ -0,0 +1,57 @@ + + Left-align indels and complex variants in VCF dataset + + macros.xml + + + + + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Left-aligns variants in VCF dataset. Window size is determined dynamically according to the entropy of the regions flanking the indel. These must have entropy > 1 bit/bp, or be shorter than ~5kb. + +---- + +Vcfleftalign @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfprimers/.shed.yml b/tool_collections/vcflib/vcfprimers/.shed.yml new file mode 100644 index 00000000000..1a00c2f626e --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Variant Analysis +description: Extract flanking sequences for each VCF record +homepage_url: https://github.com/ekg/vcflib +long_description: | + For each VCF record, extract the flanking sequences, and write them to stdout as FASTA + records suitable for alignment. This tool is intended for use in designing validation + experiments. Primers extracted which would flank all of the alleles at multi-allelic sites. +name: vcfprimers +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers +type: unrestricted diff --git a/tool_collections/vcflib/vcfprimers/macros.xml b/tool_collections/vcflib/vcfprimers/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfprimers/test-data/vcflib-phix.vcf b/tool_collections/vcflib/vcfprimers/test-data/vcflib-phix.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/test-data/vcflib-phix.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfprimers/test-data/vcflib-test-genome-phix.fa b/tool_collections/vcflib/vcfprimers/test-data/vcflib-test-genome-phix.fa new file mode 100644 index 00000000000..48a6b46678a --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/test-data/vcflib-test-genome-phix.fa @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff --git a/tool_collections/vcflib/vcfprimers/test-data/vcfprimers-test1.fasta b/tool_collections/vcflib/vcfprimers/test-data/vcfprimers-test1.fasta new file mode 100644 index 00000000000..6f5b12772b9 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/test-data/vcfprimers-test1.fasta @@ -0,0 +1,828 @@ +>phiX174_1015_LEFT +ATTCA +>phiX174_1015_RIGHT +ACTGG +>phiX174_1016_LEFT +TTCAA +>phiX174_1016_RIGHT +CTGGC +>phiX174_1038_LEFT +GCCGC +>phiX174_1038_RIGHT +TGACC +>phiX174_1045_LEFT +GACCT +>phiX174_1045_RIGHT +TCCCA +>phiX174_1048_LEFT +CTTTC +>phiX174_1048_RIGHT +CATCT +>phiX174_1050_LEFT +TTCCC +>phiX174_1050_RIGHT +TCTTG +>phiX174_1051_LEFT +TCCCA +>phiX174_1051_RIGHT +CTTGG +>phiX174_1054_LEFT +CATCT +>phiX174_1054_RIGHT +GGCTT +>phiX174_1076_LEFT +AGATT +>phiX174_1076_RIGHT +GTCGT +>phiX174_1080_LEFT +TGGTC +>phiX174_1080_RIGHT +TCTTA +>phiX174_1092_LEFT +TACCA +>phiX174_1092_RIGHT +TTCAA +>phiX174_1093_LEFT +ACCAT +>phiX174_1093_RIGHT +TCAAC +>phiX174_1102_LEFT +ACTAC +>phiX174_1102_RIGHT +CCGGT +>phiX174_1107_LEFT +TCCGG +>phiX174_1107_RIGHT +TATCG +>phiX174_1110_LEFT +GGTTA +>phiX174_1110_RIGHT +CGCTG +>phiX174_1121_LEFT +GCGAC +>phiX174_1121_RIGHT +CCTTC +>phiX174_1124_LEFT +ACTCC +>phiX174_1124_RIGHT +TCGAG +>phiX174_1125_LEFT +CTCCT +>phiX174_1125_RIGHT +CGAGA +>phiX174_1131_LEFT +CGAGA +>phiX174_1131_RIGHT +GGACG +>phiX174_1141_LEFT +GCCGT +>phiX174_1141_RIGHT +GGCGC +>phiX174_1145_LEFT +TTGGC +>phiX174_1145_RIGHT +CTCTC +>phiX174_1147_LEFT +GGCGC +>phiX174_1147_RIGHT +CTCCG +>phiX174_1149_LEFT +CGCTC +>phiX174_1149_RIGHT +CCGTC +>phiX174_1156_LEFT +CGTCT +>phiX174_1156_RIGHT +TCTCC +>phiX174_1159_LEFT +CTTTC +>phiX174_1159_RIGHT +CCATT +>phiX174_1164_LEFT +TCCAT +>phiX174_1164_RIGHT +GCGTC +>phiX174_1168_LEFT +TTGCG +>phiX174_1168_RIGHT +CGTGG +>phiX174_1171_LEFT +CGTCG +>phiX174_1171_RIGHT +GGCCT +>phiX174_1174_LEFT +CGTGG +>phiX174_1174_RIGHT +CTTGC +>phiX174_1178_LEFT +GCCTT +>phiX174_1178_RIGHT +CTATT +>phiX174_1187_LEFT +TTGAC +>phiX174_1187_RIGHT +CTACT +>phiX174_1189_LEFT +GACTC +>phiX174_1189_RIGHT +ACTGT +>phiX174_1200_LEFT +AGACA +>phiX174_1200_RIGHT +TTTTA +>phiX174_1202_LEFT +ACATT +>phiX174_1202_RIGHT +TTACT +>phiX174_1205_LEFT +TTTTT +>phiX174_1205_RIGHT +CTTTT +>phiX174_1207_LEFT +TTTAC +>phiX174_1207_RIGHT +TTTTA +>phiX174_1214_LEFT +TTTAT +>phiX174_1214_RIGHT +TCCCT +>phiX174_1216_LEFT +TATGT +>phiX174_1216_RIGHT +CCTCA +>phiX174_1217_LEFT +ATGTC +>phiX174_1217_RIGHT +CTCAT +>phiX174_1219_LEFT +GTCCC +>phiX174_1219_RIGHT +CATCG +>phiX174_1223_LEFT +CTCAT +>phiX174_1223_RIGHT +GTCAC +>phiX174_1227_LEFT +TCGTC +>phiX174_1227_RIGHT +CGTTT +>phiX174_1232_LEFT +ACGTT +>phiX174_1232_RIGHT +ATGGT +>phiX174_1236_LEFT +TTATG +>phiX174_1236_RIGHT +TGAAC +>phiX174_1237_LEFT +TATGG +>phiX174_1237_RIGHT +GAACA +>phiX174_1240_LEFT +GGTGA +>phiX174_1240_RIGHT +CAGTG +>phiX174_1245_LEFT +ACAGT +>phiX174_1245_RIGHT +GATTA +>phiX174_1247_LEFT +AGTGG +>phiX174_1247_RIGHT +TTAAG +>phiX174_1250_LEFT +GGATT +>phiX174_1250_RIGHT +AGTTC +>phiX174_1251_LEFT +GATTA +>phiX174_1251_RIGHT +GTTCA +>phiX174_1253_LEFT +TTAAG +>phiX174_1253_RIGHT +TCATG +>phiX174_1257_LEFT +GTTCA +>phiX174_1257_RIGHT +GAAGG +>phiX174_1259_LEFT +TCATG +>phiX174_1259_RIGHT +AGGAT +>phiX174_1274_LEFT +TTAAT +>phiX174_1274_RIGHT +CCACT +>phiX174_1277_LEFT +ATGCC +>phiX174_1277_RIGHT +CTCCT +>phiX174_1279_LEFT +GCCAC +>phiX174_1279_RIGHT +CCTCT +>phiX174_1284_LEFT +TCCTC +>phiX174_1284_RIGHT +CCCGA +>phiX174_1289_LEFT +TCCCG +>phiX174_1289_RIGHT +CTGTT +>phiX174_1296_LEFT +TGTTA +>phiX174_1296_RIGHT +CACTA +>phiX174_1298_LEFT +TTAAC +>phiX174_1298_RIGHT +CTACT +>phiX174_1306_LEFT +ACTGG +>phiX174_1306_RIGHT +TATAT +>phiX174_1307_LEFT +CTGGT +>phiX174_1307_RIGHT +ATATT +>phiX174_1314_LEFT +TATTG +>phiX174_1314_RIGHT +CCATG +>phiX174_1317_LEFT +TGACC +>phiX174_1317_RIGHT +TGCCG +>phiX174_1320_LEFT +CCATG +>phiX174_1320_RIGHT +CGCTT +>phiX174_1322_LEFT +ATGCC +>phiX174_1322_RIGHT +CTTTT +>phiX174_1323_LEFT +TGCCG +>phiX174_1323_RIGHT +TTTTC +>phiX174_1329_LEFT +TTTTC +>phiX174_1329_RIGHT +TGGCA +>phiX174_1335_LEFT +TGGCA +>phiX174_1335_RIGHT +GATTA +>phiX174_1338_LEFT +CACGA +>phiX174_1338_RIGHT +TAACC +>phiX174_1345_LEFT +AACCC +>phiX174_1345_RIGHT +GATAC +>phiX174_1347_LEFT +CCCTG +>phiX174_1347_RIGHT +TACCA +>phiX174_1348_LEFT +CCTGA +>phiX174_1348_RIGHT +ACCAA +>phiX174_1352_LEFT +ATACC +>phiX174_1352_RIGHT +ATAAA +>phiX174_1354_LEFT +ACCAA +>phiX174_1354_RIGHT +AAAAT +>phiX174_1359_LEFT +TAAAA +>phiX174_1359_RIGHT +CCCTA +>phiX174_1366_LEFT +CCTAA +>phiX174_1366_RIGHT +CATTT +>phiX174_1370_LEFT +AGCAT +>phiX174_1370_RIGHT +TGTTT +>phiX174_1373_LEFT +ATTTG +>phiX174_1373_RIGHT +TTCAG +>phiX174_1380_LEFT +TCAGG +>phiX174_1380_RIGHT +TTATT +>phiX174_1381_LEFT +CAGGG +>phiX174_1381_RIGHT +TATTT +>phiX174_1384_LEFT +GGTTA +>phiX174_1384_RIGHT +TTGAA +>phiX174_1385_LEFT +GTTAT +>phiX174_1385_RIGHT +TGAAT +>phiX174_1391_LEFT +TGAAT +>phiX174_1391_RIGHT +TCTAT +>phiX174_1393_LEFT +AATAT +>phiX174_1393_RIGHT +TATAA +>phiX174_1396_LEFT +ATCTA +>phiX174_1396_RIGHT +AACAA +>phiX174_1397_LEFT +TCTAT +>phiX174_1397_RIGHT +ACAAC +>phiX174_1400_LEFT +ATAAC +>phiX174_1400_RIGHT +ACTAT +>phiX174_1401_LEFT +TAACA +>phiX174_1401_RIGHT +CTATT +>phiX174_1434_LEFT +CCGTA +>phiX174_1434_RIGHT +CGAGG +>phiX174_1438_LEFT +ACCGA +>phiX174_1438_RIGHT +GCTAA +>phiX174_1450_LEFT +CCTAA +>phiX174_1450_RIGHT +GAGCT +>phiX174_1459_LEFT +CTTAA +>phiX174_1459_RIGHT +CAAGA +>phiX174_1470_LEFT +TGATG +>phiX174_1470_RIGHT +TCGTT +>phiX174_1484_LEFT +GTTTC +>phiX174_1484_RIGHT +GTTGC +>phiX174_1487_LEFT +TCCGT +>phiX174_1487_RIGHT +GCTGC +>phiX174_1491_LEFT +TTGCT +>phiX174_1491_RIGHT +CCATC +>phiX174_1503_LEFT +CAAAA +>phiX174_1503_RIGHT +CATTT +>phiX174_1536_LEFT +GACTG +>phiX174_1536_RIGHT +GCTTT +>phiX174_1541_LEFT +AGCTT +>phiX174_1541_RIGHT +CTCGC +>phiX174_1553_LEFT +AAATG +>phiX174_1553_RIGHT +CGACT +>phiX174_1566_LEFT +TACCA +>phiX174_1566_RIGHT +ATCTA +>phiX174_1572_LEFT +ATCTA +>phiX174_1572_RIGHT +TGACA +>phiX174_1574_LEFT +CTATT +>phiX174_1574_RIGHT +ACATT +>phiX174_1575_LEFT +TATTG +>phiX174_1575_RIGHT +CATTA +>phiX174_1577_LEFT +TTGAC +>phiX174_1577_RIGHT +TTATG +>phiX174_1581_LEFT +CATTA +>phiX174_1581_RIGHT +GGGTC +>phiX174_1591_LEFT +CTGCA +>phiX174_1591_RIGHT +GCTGC +>phiX174_1597_LEFT +GCTGC +>phiX174_1597_RIGHT +TATGC +>phiX174_1603_LEFT +TATGC +>phiX174_1603_RIGHT +AATTT +>phiX174_1606_LEFT +GCTAA +>phiX174_1606_RIGHT +TTGCA +>phiX174_1611_LEFT +TTTGC +>phiX174_1611_RIGHT +TACTG +>phiX174_1613_LEFT +TGCAT +>phiX174_1613_RIGHT +CTGAC +>phiX174_1618_LEFT +ACTGA +>phiX174_1618_RIGHT +CAAGA +>phiX174_1619_LEFT +CTGAC +>phiX174_1619_RIGHT +AAGAA +>phiX174_1621_LEFT +GACCA +>phiX174_1621_RIGHT +GAACG +>phiX174_1622_LEFT +ACCAA +>phiX174_1622_RIGHT +AACGT +>phiX174_1624_LEFT +CAAGA +>phiX174_1624_RIGHT +CGTGA +>phiX174_1627_LEFT +GAACG +>phiX174_1627_RIGHT +GATTA +>phiX174_1630_LEFT +CGTGA +>phiX174_1630_RIGHT +TACTT +>phiX174_1632_LEFT +TGATT +>phiX174_1632_RIGHT +CTTCA +>phiX174_1634_LEFT +ATTAC +>phiX174_1634_RIGHT +TCATG +>phiX174_1635_LEFT +TTACT +>phiX174_1635_RIGHT +CATGC +>phiX174_1639_LEFT +TTCAT +>phiX174_1639_RIGHT +CAGCG +>phiX174_1645_LEFT +CAGCG +>phiX174_1645_RIGHT +TACCg +>phiX174_1647_LEFT +GCGTT +>phiX174_1647_RIGHT +CCgTG +>phiX174_1652_LEFT +ACCgT +>phiX174_1652_RIGHT +ATGTT +>phiX174_1656_LEFT +TGATG +>phiX174_1656_RIGHT +TATTT +>phiX174_1658_LEFT +ATGTT +>phiX174_1658_RIGHT +TTTCT +>phiX174_1659_LEFT +TGTTA +>phiX174_1659_RIGHT +TTCTT +>phiX174_1663_LEFT +ATTTC +>phiX174_1663_RIGHT +TCATT +>phiX174_1665_LEFT +TTCTT +>phiX174_1665_RIGHT +ATTTG +>phiX174_1670_LEFT +CATTT +>phiX174_1670_RIGHT +GAGGT +>phiX174_1671_LEFT +ATTTG +>phiX174_1671_RIGHT +AGGTA +>phiX174_1672_LEFT +TTTGG +>phiX174_1672_RIGHT +GGTAA +>phiX174_1673_LEFT +TTGGA +>phiX174_1673_RIGHT +GTAAA +>phiX174_1674_LEFT +TGGAG +>phiX174_1674_RIGHT +TAAAA +>phiX174_1677_LEFT +AGGTA +>phiX174_1677_RIGHT +AACCT +>phiX174_1678_LEFT +GGTAA +>phiX174_1678_RIGHT +ACCTC +>phiX174_1682_LEFT +AAACC +>phiX174_1682_RIGHT +CTTAT +>phiX174_1685_LEFT +CCTCT +>phiX174_1685_RIGHT +ATGAC +>phiX174_1686_LEFT +CTCTT +>phiX174_1686_RIGHT +TGACG +>phiX174_1687_LEFT +TCTTA +>phiX174_1687_RIGHT +GACGC +>phiX174_1688_LEFT +CTTAT +>phiX174_1688_RIGHT +ACGCT +>phiX174_1689_LEFT +TTATG +>phiX174_1689_RIGHT +CGCTG +>phiX174_1691_LEFT +ATGAC +>phiX174_1691_RIGHT +CTGAC +>phiX174_1693_LEFT +GACGC +>phiX174_1693_RIGHT +GACAA +>phiX174_1695_LEFT +CGCTG +>phiX174_1695_RIGHT +CAACC +>phiX174_1702_LEFT +AACCG +>phiX174_1702_RIGHT +CCTTT +>phiX174_1707_LEFT +TCCTT +>phiX174_1707_RIGHT +ACTTG +>phiX174_1708_LEFT +CCTTT +>phiX174_1708_RIGHT +CTTGT +>phiX174_1710_LEFT +TTTAC +>phiX174_1710_RIGHT +TGTCA +>phiX174_1723_LEFT +CGCTC +>phiX174_1723_RIGHT +AATCT +>phiX174_1724_LEFT +GCTCT +>phiX174_1724_RIGHT +ATCTC +>phiX174_1725_LEFT +CTCTA +>phiX174_1725_RIGHT +TCTCT +>phiX174_1726_LEFT +TCTAA +>phiX174_1726_RIGHT +CTCTG +>phiX174_1730_LEFT +ATCTC +>phiX174_1730_RIGHT +GGGCA +>phiX174_1739_LEFT +CATCT +>phiX174_1739_RIGHT +GCTAT +>phiX174_1746_LEFT +CTATG +>phiX174_1746_RIGHT +TGTTG +>phiX174_1749_LEFT +TGATG +>phiX174_1749_RIGHT +TGATG +>phiX174_1755_LEFT +TGATG +>phiX174_1755_RIGHT +AACTG +>phiX174_1756_LEFT +GATGG +>phiX174_1756_RIGHT +ACTGA +>phiX174_1761_LEFT +AACTG +>phiX174_1761_RIGHT +CCAAA +>phiX174_1764_LEFT +TGACC +>phiX174_1764_RIGHT +AACGT +>phiX174_1766_LEFT +ACCAA +>phiX174_1766_RIGHT +CGTCG +>phiX174_1769_LEFT +AAACG +>phiX174_1769_RIGHT +CGTTA +>phiX174_1771_LEFT +ACGTC +>phiX174_1771_RIGHT +TTAGG +>phiX174_1772_LEFT +CGTCG +>phiX174_1772_RIGHT +TAGGC +>phiX174_1774_LEFT +TCGTT +>phiX174_1774_RIGHT +GGCCA +>phiX174_1775_LEFT +CGTTA +>phiX174_1775_RIGHT +GCCAG +>phiX174_1776_LEFT +GTTAG +>phiX174_1776_RIGHT +CCAGT +>phiX174_1778_LEFT +TAGGC +>phiX174_1778_RIGHT +AGTTT +>phiX174_1779_LEFT +AGGCC +>phiX174_1779_RIGHT +GTTTT +>phiX174_1781_LEFT +GCCAG +>phiX174_1781_RIGHT +TTTCT +>phiX174_1782_LEFT +CCAGT +>phiX174_1782_RIGHT +TTCTG +>phiX174_1783_LEFT +CAGTT +>phiX174_1783_RIGHT +TCTGG +>phiX174_1788_LEFT +TTCTG +>phiX174_1788_RIGHT +TCGTG +>phiX174_1792_LEFT +GGTCG +>phiX174_1792_RIGHT +GTTCA +>phiX174_1802_LEFT +AACAG +>phiX174_1802_RIGHT +CCTAT +>phiX174_1804_LEFT +CAGAC +>phiX174_1804_RIGHT +TATAA +>phiX174_1805_LEFT +AGACC +>phiX174_1805_RIGHT +ATAAA +>phiX174_1806_LEFT +GACCT +>phiX174_1806_RIGHT +TAAAC +>phiX174_1824_LEFT +GCCGC +>phiX174_1824_RIGHT +TTTCT +>phiX174_1825_LEFT +CCGCG +>phiX174_1825_RIGHT +TTCTT +>phiX174_1833_LEFT +CTTTG +>phiX174_1833_RIGHT +TCCTG +>phiX174_1843_LEFT +GAGCA +>phiX174_1843_RIGHT +GGCAC +>phiX174_1847_LEFT +ATGGC +>phiX174_1847_RIGHT +CTATG +>phiX174_1854_LEFT +TATGT +>phiX174_1854_RIGHT +TACTC +>phiX174_1860_LEFT +TACTC +>phiX174_1860_RIGHT +TGCGC +>phiX174_1863_LEFT +TCTTG +>phiX174_1863_RIGHT +GCTTG +>phiX174_1866_LEFT +TGCGC +>phiX174_1866_RIGHT +TGTTC +>phiX174_1875_LEFT +TCGTT +>phiX174_1875_RIGHT +TCCGC +>phiX174_1876_LEFT +CGTTT +>phiX174_1876_RIGHT +CCGCC +>phiX174_1882_LEFT +CCGCC +>phiX174_1882_RIGHT +ACTGC +>phiX174_1889_LEFT +CTGCG +>phiX174_1889_RIGHT +CTAAA +>phiX174_1913_LEFT +TTAAC +>phiX174_1913_RIGHT +CTAAA +>phiX174_1915_LEFT +AACGC +>phiX174_1915_RIGHT +AAAGG +>phiX174_1917_LEFT +CGCTA +>phiX174_1917_RIGHT +AGGTG +>phiX174_1930_LEFT +TTGAC +>phiX174_1930_RIGHT +TATAC +>phiX174_1934_LEFT +CTTAT +>phiX174_1934_RIGHT +CCGAT +>phiX174_1940_LEFT +CCGAT +>phiX174_1940_RIGHT +TTGCT +>phiX174_1942_LEFT +GATAT +>phiX174_1942_RIGHT +GCTGG +>phiX174_1945_LEFT +ATTGC +>phiX174_1945_RIGHT +GGCGA +>phiX174_1954_LEFT +GACCC +>phiX174_1954_RIGHT +GTTTT +>phiX174_1959_LEFT +TGTTT +>phiX174_1959_RIGHT +GTATG +>phiX174_1994_LEFT +CTATG +>phiX174_1994_RIGHT +AGGAT +>phiX174_1998_LEFT +GAAGG +>phiX174_1998_RIGHT +TGTTT diff --git a/tool_collections/vcflib/vcfprimers/tool-data/fasta_indexes.loc.sample b/tool_collections/vcflib/vcfprimers/tool-data/fasta_indexes.loc.sample new file mode 120000 index 00000000000..6d7aec6c449 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/tool-data/fasta_indexes.loc.sample @@ -0,0 +1 @@ +../../tool-data/fasta_indexes.loc.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfprimers/tool-data/tool_data_table_conf.xml.sample b/tool_collections/vcflib/vcfprimers/tool-data/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..7bfcf015ca6 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/tool-data/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../../tool-data/tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfprimers/vcfprimers.xml b/tool_collections/vcflib/vcfprimers/vcfprimers.xml new file mode 100644 index 00000000000..4402dca04c8 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/vcfprimers.xml @@ -0,0 +1,67 @@ + + Extract flanking sequences for each VCF record + + macros.xml + + + + + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +For each VCF record, extract the flanking sequences, and write them as FASTA +records suitable for alignment. This tool is intended for use in designing validation +experiments. Primers extracted which would flank all of the alleles at multi-allelic +sites. The name of the FASTA "reads" indicates the VCF record which they apply to. +The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer, +for example:: + + >20_233255_LEFT + CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA + >20_233255_RIGHT + ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA + +---- + +Vcfprimers @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfrandomsample/.shed.yml b/tool_collections/vcflib/vcfrandomsample/.shed.yml new file mode 100644 index 00000000000..a7d029682ec --- /dev/null +++ b/tool_collections/vcflib/vcfrandomsample/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Variant Analysis +description: Randomly sample sites from VCF dataset +homepage_url: https://github.com/ekg/vcflib +long_description: | + Randomly sample sites from an input VCF file. Scale the sampling + probability by the field specified by --scale-by (see advanced controls). This may be + used to provide uniform sampling across allele frequencies, for instance (AF field in this case). +name: vcfrandomsample +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample +type: unrestricted diff --git a/tool_collections/vcflib/vcfrandomsample/macros.xml b/tool_collections/vcflib/vcfrandomsample/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfrandomsample/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfrandomsample/test-data/vcflib.vcf b/tool_collections/vcflib/vcfrandomsample/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfrandomsample/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfrandomsample/test-data/vcfrandomsample-test1.vcf b/tool_collections/vcflib/vcfrandomsample/test-data/vcfrandomsample-test1.vcf new file mode 100644 index 00000000000..e2a2bd7a0b8 --- /dev/null +++ b/tool_collections/vcflib/vcfrandomsample/test-data/vcfrandomsample-test1.vcf @@ -0,0 +1,26 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##sampling="random sampling using vcfrandomsample -p 1 -r 0.2 /space/anton/galaxy-central/database/files/000/dataset_1.dat using random seed 1" +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfrandomsample/vcfrandomsample.xml b/tool_collections/vcflib/vcfrandomsample/vcfrandomsample.xml new file mode 100644 index 00000000000..4ba1ac17b44 --- /dev/null +++ b/tool_collections/vcflib/vcfrandomsample/vcfrandomsample.xml @@ -0,0 +1,54 @@ + + Randomly sample sites from VCF dataset + + macros.xml + + + + + vcfrandomsample + #if $adv_options.adv_options_selector == "use_adv_controls": + -s "${adv_options.scale_by}" + #end if + -p ${random_seed} + -r ${rate} + "${vcf_input}" > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be +used to provide uniform sampling across allele frequencies, for instance (AF field in this case). + +---- + +Vcfrandomsample @IS_PART_OF_VCFLIB@ + + + diff --git a/tool_collections/vcflib/vcfselectsamples/.shed.yml b/tool_collections/vcflib/vcfselectsamples/.shed.yml new file mode 100644 index 00000000000..5f3f6197a41 --- /dev/null +++ b/tool_collections/vcflib/vcfselectsamples/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: Select samples from a VCF file +homepage_url: https://github.com/ekg/vcflib +long_description: | + Allows selecting samples from a VCF dataset. This tool combines + vcfkeepsamples and vcfremovesamples from VCFlib package into a single utility. +name: vcfselectsamples +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples +type: unrestricted diff --git a/tool_collections/vcflib/vcfselectsamples/macros.xml b/tool_collections/vcflib/vcfselectsamples/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfselectsamples/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfselectsamples/test-data/vcflib.vcf b/tool_collections/vcflib/vcfselectsamples/test-data/vcflib.vcf new file mode 100644 index 00000000000..e8dd794d9bd --- /dev/null +++ b/tool_collections/vcflib/vcfselectsamples/test-data/vcflib.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 diff --git a/tool_collections/vcflib/vcfselectsamples/test-data/vcfselectsamples-test1.vcf b/tool_collections/vcflib/vcfselectsamples/test-data/vcfselectsamples-test1.vcf new file mode 100644 index 00000000000..01f2a43aeaa --- /dev/null +++ b/tool_collections/vcflib/vcfselectsamples/test-data/vcfselectsamples-test1.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 1/1:40:3 +20 1235237 . T . 0 . . GT 0/0 ./. +X 10 rsTest AC A,ATG 10 PASS . GT 0 0|2 diff --git a/tool_collections/vcflib/vcfselectsamples/vcfselectsamples.xml b/tool_collections/vcflib/vcfselectsamples/vcfselectsamples.xml new file mode 100644 index 00000000000..d66dbd537d7 --- /dev/null +++ b/tool_collections/vcflib/vcfselectsamples/vcfselectsamples.xml @@ -0,0 +1,53 @@ + + Select samples from a VCF dataset + + macros.xml + + + + vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}" + + + + + + + + + + + + + + + + + + + + +Allows to keep or remove samples from a VCF file. + +----- + +.. class:: infomark + + +**Example**: + +Selecting *NA00001* and *NA00003* from the following VCF line:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 + 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. + +will, obviously, remove *NA00002*:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 + 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. + +---- + +Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + + diff --git a/tool_collections/vcflib/vcfsort/.shed.yml b/tool_collections/vcflib/vcfsort/.shed.yml new file mode 100644 index 00000000000..dc5ac2efe83 --- /dev/null +++ b/tool_collections/vcflib/vcfsort/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Variant Analysis +description: Sort VCF dataset by coordinate +long_description: | + This tools uses native UNIX sort command to order VCF dataset in coordinate order. +name: vcfsort +owner: devteam +homepage_url: https://github.com/ekg/vcflib +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort +type: unrestricted diff --git a/tool_collections/vcflib/vcfsort/macros.xml b/tool_collections/vcflib/vcfsort/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfsort/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfsort/test-data/vcfsort-test1-input.vcf b/tool_collections/vcflib/vcfsort/test-data/vcfsort-test1-input.vcf new file mode 100644 index 00000000000..22a28296937 --- /dev/null +++ b/tool_collections/vcflib/vcfsort/test-data/vcfsort-test1-input.vcf @@ -0,0 +1,30 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 diff --git a/tool_collections/vcflib/vcfsort/test-data/vcfsort-test1.vcf b/tool_collections/vcflib/vcfsort/test-data/vcfsort-test1.vcf new file mode 100644 index 00000000000..e41d940304f --- /dev/null +++ b/tool_collections/vcflib/vcfsort/test-data/vcfsort-test1.vcf @@ -0,0 +1,30 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . . . . GT 0/0 0|0 ./. diff --git a/tool_collections/vcflib/vcfsort/vcfsort.xml b/tool_collections/vcflib/vcfsort/vcfsort.xml new file mode 100644 index 00000000000..bf66bf24f8a --- /dev/null +++ b/tool_collections/vcflib/vcfsort/vcfsort.xml @@ -0,0 +1,30 @@ + + Sort VCF dataset by coordinate + + macros.xml + + "${out_file1}" + ]]> + + + + + + + + + + + + + +This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is:: + + (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file + +.. class:: infomark + +The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). + + diff --git a/tool_collections/vcflib/vcfvcfintersect/.shed.yml b/tool_collections/vcflib/vcfvcfintersect/.shed.yml new file mode 100644 index 00000000000..04e1c655f4e --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Variant Analysis +description: Intersect two VCF datasets +homepage_url: https://github.com/ekg/vcflib +long_description: | + Computes intersections and unions for two VCF datasets. Unifies + equivalent alleles within window-size bp. +name: vcfvcfintersect +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect +type: unrestricted diff --git a/tool_collections/vcflib/vcfvcfintersect/macros.xml b/tool_collections/vcflib/vcfvcfintersect/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/vcflib/vcfvcfintersect/test-data/vcflib-test-genome-phix.fa b/tool_collections/vcflib/vcfvcfintersect/test-data/vcflib-test-genome-phix.fa new file mode 100644 index 00000000000..48a6b46678a --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/test-data/vcflib-test-genome-phix.fa @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff --git a/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-input1.vcf b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-input1.vcf new file mode 100644 index 00000000000..ff8bfd3b023 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-input1.vcf @@ -0,0 +1,121 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, diff --git a/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-input2.vcf b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-input2.vcf new file mode 100644 index 00000000000..3e204c5b440 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-input2.vcf @@ -0,0 +1,122 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-test1.vcf b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-test1.vcf new file mode 100644 index 00000000000..ac48f7398d2 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-test1.vcf @@ -0,0 +1,24 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, diff --git a/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-test2.vcf b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-test2.vcf new file mode 100644 index 00000000000..362e6be2088 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/test-data/vcfvcfintersect-test2.vcf @@ -0,0 +1,219 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1, +phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2, +phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30, +phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2, +phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1, +phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3, +phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1, +phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1, +phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36, +phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39, +phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1, +phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52, +phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50, +phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2, +phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1, +phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3, +phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1, +phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1, +phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57, +phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2, +phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52, +phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50, +phiX174 1149 . T G,C 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54, +phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2, +phiX174 1159 . T C,G 0 . AC=2,2;AF=0.0298507462687,0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2, +phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4, +phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1, +phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38, +phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38, +phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41, +phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44, +phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1, +phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3, +phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1, +phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2, +phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45, +phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45, +phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46, +phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2, +phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44, +phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40, +phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2, +phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35, +phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1, +phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1, +phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32, +phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35, +phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39, +phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3, +phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2, +phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2, +phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1, +phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44, +phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1, +phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2, +phiX174 1284 . T G,C 0 . AC=3,2;AF=0.038961038961,0.025974025974 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37, +phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1, +phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2, +phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1, +phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25, +phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27, +phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3, +phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35, +phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36, +phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40, +phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2, +phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1, +phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45, +phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40, +phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1, +phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43, +phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43, +phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2, +phiX174 1354 . T G,A 0 . AC=2,2;AF=0.027027027027,0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1, +phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1, +phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28, +phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2, +phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25, +phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32, +phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31, +phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1, +phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29, +phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1, +phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32, +phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32, +phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2, +phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31, +phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31, +phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21, +phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21, +phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1, +phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19, +phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21, +phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25, +phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26, +phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26, +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, +phiX174 1603 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=50, +phiX174 1606 . T G 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0666666666667:A=1,C=1,T=28,G=2, 0:0:0:T=52, +phiX174 1611 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=56,C=1, +phiX174 1613 . A G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:0:0:A=25,C=1,G=1, 0:2:0.0344827586207:A=56,G=2, +phiX174 1618 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28,G=1, 0:0:0:A=1,C=57, +phiX174 1619 . C A 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0666666666667:A=2,C=28, 0:0:0:C=57, +phiX174 1621 . A C 0 . AC=3;AF=0.0352941176471 GT:AC:AF:NC 0:0:0:A=31,T=1,G=1, 0:3:0.0555555555556:A=51,C=3, +phiX174 1622 . G T 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0:0:A=1,G=35, 0:2:0.037037037037:T=2,G=52, +phiX174 1624 . A G 0 . AC=2;AF=0.0235294117647 GT:AC:AF:NC 0:2:0.0555555555556:A=34,T=1,G=2, 0:0:0:A=49, +phiX174 1627 . T G,C 0 . AC=2,2;AF=0.0246913580247,0.0246913580247 GT:AC:AF:NC 0:0,0:0,0:T=37,G=1, 0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2, +phiX174 1630 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0526315789474:C=1,T=36,G=2, 0:0:0:T=40, +phiX174 1632 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=41, +phiX174 1634 . T G 0 . AC=4;AF=0.0493827160494 GT:AC:AF:NC 0:2:0.047619047619:C=1,T=40,G=2, 0:2:0.0512820512821:T=37,G=2, +phiX174 1635 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=40, +phiX174 1639 . G A 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.075:A=3,T=1,G=37, 0:0:0:G=34, +phiX174 1645 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0425531914894:T=45,G=2, 0:0:0:T=27,G=1, +phiX174 1647 . A T,G,C 0 . AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962 GT:AC:AF:NC 0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2, 0:2,0,0:0.0740740740741,0,0:A=25,T=2, +phiX174 1652 . G A 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.037037037037:A=2,G=52, 0:0:0:G=29, +phiX174 1656 . T G 0 . AC=3;AF=0.0348837209302 GT:AC:AF:NC 0:3:0.0555555555556:T=51,G=3, 0:0:0:T=32,G=1, +phiX174 1658 . A C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.04:A=48,C=2, 0:0:0:A=33, +phiX174 1659 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0625:C=1,T=45,G=3, 0:0:0:T=34, +phiX174 1663 . T G 0 . AC=4;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=1,T=53, 0:4:0.114285714286:T=31,G=4, +phiX174 1665 . C A 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:A=2,C=50,G=1, 0:0:0:C=42, +phiX174 1670 . G C 0 . AC=2;AF=0.0224719101124 GT:AC:AF:NC 0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47, 0:0,0:0,0:T=1,G=40, +phiX174 1671 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0384615384615:C=1,T=2,G=50, 0:0:0:G=42, +phiX174 1672 . A G 0 . AC=3;AF=0.0315789473684 GT:AC:AF:NC 0:3:0.0545454545455:A=52,G=3, 0:0:0:A=40,T=1, +phiX174 1673 . G T 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:2:0.0377358490566:C=1,T=2,G=51, 0:0:0:G=41, +phiX174 1674 . G T 0 . AC=4;AF=0.04 GT:AC:AF:NC 0:4:0.0714285714286:T=4,G=52, 0:0:0:G=44, +phiX174 1677 . A C 0 . AC=3;AF=0.031914893617 GT:AC:AF:NC 0:3:0.0566037735849:A=50,C=3,N=1, 0:0:0:A=41, +phiX174 1678 . A C 0 . AC=2;AF=0.0212765957447 GT:AC:AF:NC 0:0:0:A=54,C=1,G=1, 0:2:0.05:A=38,C=2, +phiX174 1682 . T C 0 . AC=2;AF=0.0229885057471 GT:AC:AF:NC 0:2:0.0408163265306:C=2,T=47,G=1, 0:0:0:C=1,T=38, +phiX174 1685 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.046511627907:A=1,T=41,G=2, 0:0:0:T=41,G=1, +phiX174 1686 . A C 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:A=39,C=1,T=1,G=1, 0:2:0.0512820512821:A=37,C=2, +phiX174 1687 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.047619047619:C=2,T=40, 0:0:0:A=1,T=40, +phiX174 1688 . G C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=41, +phiX174 1689 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2,T=1,G=1, 0:0:0:A=41,C=1, +phiX174 1691 . G C 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.05:C=2,T=1,G=38, 0:0:0:G=37, +phiX174 1693 . T G 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0:0:T=42,G=1, 0:2:0.047619047619:T=40,G=2, +phiX174 1695 . A C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.046511627907:A=41,C=2, 0:0:0:A=43,C=1, +phiX174 1702 . T C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0512820512821:A=1,C=2,T=37, 0:0:0:C=1,T=42, +phiX174 1707 . T C 0 . AC=2;AF=0.0232558139535 GT:AC:AF:NC 0:2:0.05:C=2,T=38, 0:0:0:T=46,G=1, +phiX174 1708 . A C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:2:0.0526315789474:A=36,C=2, 0:0:0:A=46,C=1,G=1, +phiX174 1710 . T C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:0:0:C=1,T=34, 0:2:0.0434782608696:C=2,T=44, +phiX174 1723 . T C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0588235294118:C=2,T=32, 0:0:0:T=48, +phiX174 1724 . A C 0 . AC=4;AF=0.0481927710843 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:2:0.0416666666667:A=46,C=2, +phiX174 1725 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0606060606061:A=31,C=2, 0:0:0:A=49, +phiX174 1726 . T G 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:C=1,T=47, +phiX174 1730 . T G 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:C=1,T=28, 0:2:0.0444444444444:T=43,G=2, +phiX174 1739 . G T 0 . AC=3;AF=0.0434782608696 GT:AC:AF:NC 0:3:0.09375:T=3,G=29, 0:0:0:G=37, +phiX174 1746 . A C 0 . AC=2;AF=0.0338983050847 GT:AC:AF:NC 0:2:0.0689655172414:A=27,C=2, 0:0:0:A=30,C=1,G=1, +phiX174 1749 . T G,C 0 . AC=3,2;AF=0.044776119403,0.0298507462687 GT:AC:AF:NC 0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3, 0:0,0:0,0:T=32,G=1, +phiX174 1755 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.05:C=2,G=38, 0:0:0:C=1,G=33, +phiX174 1756 . A G,C 0 . AC=2,2;AF=0.0281690140845,0.0281690140845 GT:AC:AF:NC 0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1, 0:2,0:0.0606060606061,0:A=31,C=1,G=2, +phiX174 1761 . A G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=1,G=2, 0:0:0:A=31, +phiX174 1764 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=28, +phiX174 1766 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0487804878049:A=39,C=2, 0:0:0:A=27, +phiX174 1769 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0526315789474:A=1,C=1,T=36,G=2, 0:0:0:T=26,G=1, +phiX174 1771 . G C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0526315789474:C=2,G=36, 0:0:0:G=29, +phiX174 1772 . T G 0 . AC=4;AF=0.0597014925373 GT:AC:AF:NC 0:4:0.108108108108:C=1,T=33,G=4, 0:0:0:T=30, +phiX174 1774 . A G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0810810810811:A=34,G=3, 0:0:0:A=31, +phiX174 1775 . G A 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=2,G=33, 0:0:0:G=31, +phiX174 1776 . G T 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0540540540541:T=2,G=35, 0:0:0:G=32, +phiX174 1778 . C G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0526315789474:C=36,G=2, 0:0:0:C=31, +phiX174 1779 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:A=37,C=3, 0:0:0:A=28, +phiX174 1781 . T G 0 . AC=5;AF=0.0714285714286 GT:AC:AF:NC 0:2:0.0487804878049:C=1,T=39,G=2, 0:3:0.103448275862:T=26,G=3, +phiX174 1782 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.075:T=37,G=3, 0:0:0:A=1,T=28, +phiX174 1783 . T C 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2:0.0512820512821:C=2,T=37, 0:0:0:T=28,G=1, +phiX174 1788 . G T 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:0:0:A=1,T=1,G=29, 0:2:0.0689655172414:T=2,G=27, +phiX174 1792 . T G 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:T=25,G=1, +phiX174 1802 . A C 0 . AC=2;AF=0.030303030303 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=31,C=1, +phiX174 1804 . C T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0588235294118:A=1,C=32,T=2, 0:0:0:C=34, +phiX174 1805 . T G 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0857142857143:T=32,G=3, 0:0:0:T=33,G=1, +phiX174 1806 . A C 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=34,G=1, +phiX174 1824 . G C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0714285714286:C=2,T=1,G=26, 0:0:0:G=43, +phiX174 1825 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=42,G=1, +phiX174 1833 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0444444444444:T=43,G=2, +phiX174 1843 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.08:A=1,T=23,G=2, 0:0:0:T=38, +phiX174 1847 . A C 0 . AC=2;AF=0.0333333333333 GT:AC:AF:NC 0:2:0.0833333333333:A=22,C=2,T=1,G=1, 0:0:0:A=36, +phiX174 1854 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0487804878049:T=39,G=2, +phiX174 1860 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:0:0:A=1,T=20, 0:2:0.0606060606061:T=31,G=2, +phiX174 1863 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=17,G=2, 0:0:0:C=33, +phiX174 1866 . T G 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:T=19,G=1, 0:2:0.0645161290323:T=29,G=2, +phiX174 1875 . T A 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.0952380952381:A=2,T=19, 0:0:0:T=32,G=1, +phiX174 1876 . T G 0 . AC=3;AF=0.0588235294118 GT:AC:AF:NC 0:3:0.157894736842:C=1,T=16,G=3, 0:0:0:T=32,G=1, +phiX174 1882 . T G 0 . AC=2;AF=0.0377358490566 GT:AC:AF:NC 0:2:0.105263157895:T=17,G=2, 0:0:0:T=34, +phiX174 1889 . A C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:2:0.0869565217391:A=21,C=2, 0:0:0:A=27, +phiX174 1913 . G C 0 . AC=2;AF=0.04 GT:AC:AF:NC 0:0:0:G=27, 0:2:0.0869565217391:C=2,G=21, +phiX174 1915 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:A=1,T=24, 0:2:0.0869565217391:T=21,G=2, +phiX174 1917 . A T 0 . AC=2;AF=0.0444444444444 GT:AC:AF:NC 0:2,0:0.0833333333333,0:A=22,T=2,G=1, 0:0,0:0,0:A=21,G=1, +phiX174 1930 . T A 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0909090909091:A=2,T=20, 0:0:0:T=16, +phiX174 1934 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2,T=1, 0:0:0:A=18,C=1, +phiX174 1940 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=2, 0:0:0:A=22,C=1, +phiX174 1942 . T G 0 . AC=2;AF=0.047619047619 GT:AC:AF:NC 0:0:0:T=19, 0:2:0.0869565217391:T=21,G=2, +phiX174 1945 . T G 0 . AC=3;AF=0.0769230769231 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:3:0.125:T=21,G=3, +phiX174 1954 . T C 0 . AC=2;AF=0.0625 GT:AC:AF:NC 0:0,0:0,0:T=12,G=1, 0:0,2:0,0.1:C=2,T=18,G=1, +phiX174 1959 . T G 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=23, +phiX174 1994 . A C 0 . AC=2;AF=0.0512820512821 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=26, +phiX174 1998 . A G 0 . AC=2;AF=0.05 GT:AC:AF:NC 0:2:0.142857142857:A=12,G=2, 0:0:0:A=26, diff --git a/tool_collections/vcflib/vcfvcfintersect/tool-data/fasta_indexes.loc.sample b/tool_collections/vcflib/vcfvcfintersect/tool-data/fasta_indexes.loc.sample new file mode 120000 index 00000000000..6d7aec6c449 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/tool-data/fasta_indexes.loc.sample @@ -0,0 +1 @@ +../../tool-data/fasta_indexes.loc.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfvcfintersect/tool-data/tool_data_table_conf.xml.sample b/tool_collections/vcflib/vcfvcfintersect/tool-data/tool_data_table_conf.xml.sample new file mode 120000 index 00000000000..7bfcf015ca6 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/tool-data/tool_data_table_conf.xml.sample @@ -0,0 +1 @@ +../../tool-data/tool_data_table_conf.xml.sample \ No newline at end of file diff --git a/tool_collections/vcflib/vcfvcfintersect/vcfvcfintersect.xml b/tool_collections/vcflib/vcfvcfintersect/vcfvcfintersect.xml new file mode 100644 index 00000000000..129e5a5ab23 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/vcfvcfintersect.xml @@ -0,0 +1,128 @@ + + Intersect two VCF datasets + + macros.xml + + + + + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + #if $adv_options.adv_options_selector == "use_adv_controls": + vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" + #else: + vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. + +The options are:: + + -v, --invert invert the selection, printing only records which would + -i, --intersect-vcf FILE use this VCF for set intersection generation + -u, --union-vcf FILE use this VCF for set union generation + -w, --window-size N compare records up to this many bp away (default 30) + -l, --loci output whole loci when one alternate allele matches + -m, --ref-match intersect on the basis of record REF string + -t, --tag TAG attach TAG to each record's info field if it would intersect + -V, --tag-value VAL use this value to indicate that the allele is passing + '.' will be used otherwise. default: 'PASS' + -M, --merge-from FROM-TAG + -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG + in the current file. + +---- + +VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + +