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 journalArticle

2472 Citations (Scopus)

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 languageEnglish (US)
Article numberbtr330
Pages (from-to)2156-2158
Number of pages3
JournalBioinformatics
Volume27
Issue number15
DOIs
StatePublished - Aug 2011
Externally publishedYes

Fingerprint

Genome
Genes
Exome
National Heart, Lung, and Blood Institute (U.S.)
Information Storage and Retrieval
Polymorphism
Application programming interfaces (API)
Merging
Deletion
Insertion
Single Nucleotide Polymorphism
Annotation
Retrieval
DNA
Software
Processing
Range of data

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., ... Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. [btr330]. https://doi.org/10.1093/bioinformatics/btr330

The variant call format and VCFtools. / Danecek, Petr; Auton, Adam; Abecasis, Goncalo; Albers, Cornelis A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Lunter, Gerton; Marth, Gabor T.; Sherry, Stephen T.; McVean, Gilean; Durbin, Richard.

In: Bioinformatics, Vol. 27, No. 15, btr330, 08.2011, p. 2156-2158.

Research output: Contribution to journalArticle

Danecek, P, Auton, A, Abecasis, G, Albers, CA, Banks, E, DePristo, MA, Handsaker, RE, Lunter, G, Marth, GT, Sherry, ST, McVean, G & Durbin, R 2011, 'The variant call format and VCFtools', Bioinformatics, vol. 27, no. 15, btr330, pp. 2156-2158. https://doi.org/10.1093/bioinformatics/btr330
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA et al. The variant call format and VCFtools. Bioinformatics. 2011 Aug;27(15):2156-2158. btr330. https://doi.org/10.1093/bioinformatics/btr330
Danecek, Petr ; Auton, Adam ; Abecasis, Goncalo ; Albers, Cornelis A. ; Banks, Eric ; DePristo, Mark A. ; Handsaker, Robert E. ; Lunter, Gerton ; Marth, Gabor T. ; Sherry, Stephen T. ; McVean, Gilean ; Durbin, Richard. / The variant call format and VCFtools. In: Bioinformatics. 2011 ; Vol. 27, No. 15. pp. 2156-2158.
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