README.md

Name

vcfparse.py

Description

Parses a VCF file and extracts the specified regions.

Dependencies

Python Modules

• PyVCF

• argparse

  _{* only if using a Python version < 2.7}

Synopsis

vcfparse vcf_file [field1 field2 ... fieldN] [-h]

Arguments

• vcf_file: the VCF file to parse
• fields: a list of fields to extract from the VCF file.

Options

• --help, -h: print a helpful message and exit.

Examples

A command such as

vcfparse test.vcf gq dp sdp ad

will create four separate text files, one for each field. Each text file has a header of the form

Chromosome  Position    Value   Sample

which is tab separated and each subsequent line will look something like this

chr10   181479  27  Sample4

Thanks

Thanks to the people who have contributed to PyVCF for allowing me to write way less than one hundred lines of code:)