Documentation for beddows-vrc.pl.
Author: Ian Beddows 12/17/2017.
Contact: beddowsi4@gmail.com.
Tested 17 Dec 2017 on MAC OS X El Capitan v10.11.2.
The program has two perl module dependencies:
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JSON.pm
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Getopt/Long.pm
This program takes a VCF file, extracts some of its information (see below) and returns it into a .txt file. Two pieces of information from the ExAC database (exac.broadinstitute.org) are also reported:
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The most deleterious variant effect.
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Whether or not the variant is found in the ExAC database.
To run this program on the command line type: perl beddows-vrc.pl -i path/to/vcf/file.vcf
The -o option can also be used to specify the outfile (defaults to results.txt)
Requires a VCFv4.2 file.
Requires the following IDs in column 8 of the VCF: TYPE, DP, AF, AO, and RO.
The results.txt file has 1 row per variant and 9 columns:
1) chr
2) pos
3) variant_type
4) variant_effect # from the ExAC database
5) total_read_depth
6) n_reads_supporting_variant
7) perc_reads_supporting_variant # relative to those supporting the reference
8) variant_allele_freq
9) any_covered # from the ExAC database (true if this variant is found in individuals in the database)