vcf_annotate

Description

A prototype VCF parser and ExAC annotation tool. In the command line interface, the user supplies a VCF file (v4.1) to the module, which returns an annotated CSV file, with additional variant information columns extracted via the ExAC database API.

ExAC API can be found here:

http://exac.hms.harvard.edu/

Each variant has the following information:

• var_type: type of variation (complex, insertion, deletion, etc.)
• VEP: genotype consequence (missense, synonymous, etc.)
• depth: depth of sequence coverage at the site of variation
• num_reads: number of reads supporting the variant versus those supporting reference reads
• percent_variant_support: percent of reads supporting variant
• exac_allele_freq: allele frequency, from ExAC

Note: If there are multiple variant effects, the annotation is the most deleterious one. Script contains an ordered list of variant effect severity from Ensembl.

Usage

Command line:

• Names in < > are for the user to replace with the appropriate file names.

python3 vcf_parser_prototype.py <INPUT.vcf> <OUTPUT_FILE_NAME>

An Internet connection is required to query via the ExAC API.

Dependencies

See environment.yml