cyvcf2: fast, flexible variant analysis with Python

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Abstract

Motivation:

Variant call format (VCF) files document the genetic variation observed after DNA sequencing, alignment and variant calling of a sample cohort. Given the complexity of the VCF format as well as the diverse variant annotations and genotype metadata, there is a need for fast, flexible methods enabling intuitive analysis of the variant data within VCF and BCF files.

Results:

We introduce cyvcf2, a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.

Contact:

bpederse@gmail.com or aaronquinlan@gmail.com

Availability and Implementation:

cyvcf2 is available from https://github.com/brentp/cyvcf2 under the MIT license and from common python package managers. Detailed documentation is available at http://brentp.github.io/cyvcf2/

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