Annotate VCF

Annotate variant VCF file with the following:

1. Read depth.
2. Number of reads supporting alternative allele.
3. Percent reads that support alternative allele over total reads.
4. ExAC frequency.
5. Most severe onsequence annotation using [VEP API] (https://rest.ensembl.org)
6. Variant type (substitution, insertion, CNV, etc.).

link to repository: https://bitbucket.org/stara/variant_annotation/src/master/

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Example usage:

python code/VCF_reader.py data/Challenge_data_(1).vcf output/final_output.txt

My personal laptop is still using python 2.7 so that is what I used.

python --version

Python 2.7.14 :: Anaconda, Inc.

package requirements listed in requirements.txt