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Document running the tools and any bwa mem options #11

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nh13 opened this issue Apr 6, 2022 · 0 comments
Open

Document running the tools and any bwa mem options #11

nh13 opened this issue Apr 6, 2022 · 0 comments
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@clintval
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documentation Improvements or additions to documentation

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nh13 commented Apr 6, 2022

Requirements:

  • run bwa mem:
    • without the -M option (-M marks shorter split hits as secondary).
    • use the -Y option (use soft clipping for supplementary alignments).

Run:

  • fgsv SvPileup -i <input.bam> -o <out-pre>.raw
  • fgsv AggregateSvPileup -i <out-pre>.raw.txt -o <out_pre>.final.txt
@nh13 nh13 added the documentation Improvements or additions to documentation label Apr 6, 2022
@clintval clintval self-assigned this Nov 28, 2023
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