cyvcf2: fast, flexible variant analysis with Python

    loading  Checking for direct PDF access through Ovid



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.


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: or

Availability and Implementation:

cyvcf2 is available from under the MIT license and from common python package managers. Detailed documentation is available at

Related Topics

    loading  Loading Related Articles