The variant call format and VCFtools

Petr Danecek(Broad Institute), Adam Auton(Broad Institute), Gonçalo R. Abecasis(Broad Institute), Cornelis A. Albers(Broad Institute), Eric Banks(Broad Institute), Mark A. DePristo(Broad Institute), Robert E. Handsaker(Broad Institute), Gerton Lunter(Broad Institute), Gábor Marth(Broad Institute), Stephen T. Sherry(Broad Institute), Gil McVean(Broad Institute), Richard Durbin(Broad Institute), 1000 Genomes Project Analysis Group
Bioinformatics
June 7, 2011
10.1093/bioinformatics/btr330
Cited by 17,596Open Access
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Abstract

SUMMARY: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. AVAILABILITY: http://vcftools.sourceforge.net

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