cyvcf2: fast, flexible variant analysis with Python

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...

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Bibliographic Details
Published inBioinformatics (Oxford, England) Vol. 33; no. 12; pp. 1867 - 1869
Main Authors Pedersen, Brent S, Quinlan, Aaron R
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.06.2017
Subjects
Applications Notes
Genetic Variation
Genotyping Techniques - methods
Humans
Metadata
Sequence Analysis, DNA - methods
Software
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Summary: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. bpederse@gmail.com or aaronquinlan@gmail.com. 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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ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btx057