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cyvcf2: fast, flexible variant analysis with Python

2017; Oxford University Press; Volume: 33; Issue: 12 Linguagem: Inglês

10.1093/bioinformatics/btx057

ISSN

1367-4811

Autores

Brent S. Pedersen, Aaron R. Quinlan,

Tópico(s)

Gene expression and cancer classification

Resumo

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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