The variant call format and VCFtools

Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A. Albers; Eric Banks; Mark A. DePristo; Robert E. Handsaker; Gerton Lunter; Gabor T. Marth; Stephen T. Sherry; Gilean McVean; Richard Durbin

doi:10.1093/bioinformatics/btr330

The variant call format and VCFtools

Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin

Research output: Contribution to journal › Article › peer-review

8370 Scopus citations

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.

Original language	English (US)
Article number	btr330
Pages (from-to)	2156-2158
Number of pages	3
Journal	Bioinformatics
Volume	27
Issue number	15
DOIs	https://doi.org/10.1093/bioinformatics/btr330
State	Published - Aug 2011
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr330

Cite this

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title = "The variant call format and VCFtools",

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.",

author = "Petr Danecek and Adam Auton and Goncalo Abecasis and Albers, {Cornelis A.} and Eric Banks and DePristo, {Mark A.} and Handsaker, {Robert E.} and Gerton Lunter and Marth, {Gabor T.} and Sherry, {Stephen T.} and Gilean McVean and Richard Durbin",

note = "Funding Information: Funding: Medical Research Council, UK; British Heart Foundation (grant RG/09/012/28096); Wellcome Trust (grants 090532/Z/09/Z and 075491/Z/04); National Human Genome Research Institute (grants 54 HG003067, R01 HG004719 and U01 HG005208); Intramural Research Program of the National Institutes of Health, the National Library of Medicine.",

year = "2011",

month = aug,

doi = "10.1093/bioinformatics/btr330",

language = "English (US)",

volume = "27",

pages = "2156--2158",

journal = "Bioinformatics",

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AU - Danecek, Petr

AU - Auton, Adam

AU - Abecasis, Goncalo

AU - Albers, Cornelis A.

AU - Banks, Eric

AU - DePristo, Mark A.

AU - Handsaker, Robert E.

AU - Lunter, Gerton

AU - Marth, Gabor T.

AU - Sherry, Stephen T.

AU - McVean, Gilean

AU - Durbin, Richard

N1 - Funding Information: Funding: Medical Research Council, UK; British Heart Foundation (grant RG/09/012/28096); Wellcome Trust (grants 090532/Z/09/Z and 075491/Z/04); National Human Genome Research Institute (grants 54 HG003067, R01 HG004719 and U01 HG005208); Intramural Research Program of the National Institutes of Health, the National Library of Medicine.

PY - 2011/8

Y1 - 2011/8

N2 - 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.

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The variant call format and VCFtools

Abstract

ASJC Scopus subject areas

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