cyvcf2: fast, flexible variant analysis with Python.
BACKGROUND
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.


BACKGROUND
bpederse@gmail.com or aaronquinlan@gmail.com.


METHODS
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/.
Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
Brent S
BS
Pedersen
Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
Aaron R
AR
Quinlan
D014644:Genetic Variation; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D000071253:Metadata; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software