Sentieon's vcflib

An open-source Python library for parsing and manipulation of variant call format (VCF) files.

Installation

Install with pip:

pip install vcflib

Highlights

• Transparently supports reading and writing uncompressed or bgzip-compressed and tabix-indexed VCF files.
• VCF and gVCF (with the .g.vcf.gz suffix) files are supported.
• Output files write tribble (.vcf.idx) and tabix (vcf.gz.tbi) indexes on the fly, without a separate pass through the data for indexing.
• Parallelization across genomic regions is supported with a Sharder class.
• Support for Python2.7 and Python3.

Example Usuage - VCF filtering

A simple script that filters variants with a DP < 10 from an input VCF is provided as an example at example/filter_dp.py.

python example/filter_dp.py --input_vcf <VCF> --output_vcf <VCF>

Contributing

Thank you for your interest in contributing to vcflib, we welcome community contributions! The source files for vcflib are currently maintained in an internal codebase, and pull requests cannot be merged directly, although they will be reviewed by our team.