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Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

The variant call format and VCFtools.

Collaborators (743)

Durbin R, Altshuler D, Abecasis G, Bentley D, Chakravarti A, Clark A, De La Vega F, Donnelly P, Dunn M, Flicek P, Gabriel S, Green E, Gibbs R, Knoppers B, Lander E, Lehrach H, Mardis E, Marth G, McVean G, Nickerson D, Schmidt J, Sherry S, Wang J, Wilson R, Knoppers B, Chakravarti A, Abecasis G, Barnes K, Bedoya G, Brooks L, Bull S, Burchard E, Bustamante C, Clemm N, Conway D, Corrah T, De La Vega F, Dunstan S, Dutil J, Gallo C, Garcia-Montero A, Gharani N, Gibbs R, Gignoux C, Gravel S, Henn B, Heyderman R, Humphray S, Jallow M, Jorde L, Kaye J, Keinan A, Kent A, Kumarasamy T, Kwiatkowski D, Lee C, Li R, Li T, Martinez-Cruzado JC, Mathias R, McGuire A, McVean G, McEwen J, Moreno A, Mullikin J, Oleksyk T, Ossorio P, Parker M, Parra V, Poletti G, Presgraves D, Reich D, Rotimi C, Ruiz-Linares A, Saleheen D, Joof FS, Su Y, Sudbrak R, Taylor H, Timmermann B, Tishkoff S, Toji L, Tyler-Smith C, Via M, Wang W, Wilson J, Yang G, Yang L, Mardis E, Gabriel S, Abecasis G, Ambrogio L, Balasubramaniam S, Belaia Z, Bentley D, Blackwell T, Borodina T, Brooks L, Cibulskis K, Clarke L, Clemm N, Coffrey A, Costa G, Dahl A, Danecek P, De La Vega F, Danecek P, Durbin R, Felsenfeld A, Fennell T, Flicek P, Fulton L, Gibbs R, Humphray S, Indap A, Iqbal Z, Jaffe D, Katzman S, Keane T, Kuhn R, Li R, McCarthy S, McKernan K, McVean G, Metzker M, Mertes F, Muzny D, Nickerson E, Nusbaum C, Palotie A, Reid J, Shefler E, Sherry S, Shumway M, Smith R, Soldatov A, Sougnez C, Stalker J, Sudbrak R, Swerdlow H, Timmermann B, Wang J, Weinstock G, Wilson R, Xiao C, Yang H, Bradley HZ, McVean G, Abecasis G, Abyzov A, Agarwala R, Albers K, Alkan C, Altshuler D, Amstislavskiy V, Anderson P, del Angel G, Arbiza L, Auton A, Awadalla P, Ayub Q, Bafna V, Bainbridge M, Balasubramaniam S, Ball A, Ball E, Balasubramanian S, Banks E, Barrett J, Bashir A, Batzer M, Bauer M, Bentley D, Birney E, Blackburne B, Blackwell T, Blekhman R, Bloom T, Boyko A, Bonnen P, Brisbin A, Brooks L, Browning B, Browning S, Bustamante C, Byrnes J, Cappellieri A, Caccamo M, Cardin N, Chakravarti A, Challis D, Cheetham K, Chen K, Chen Y, Chen W, Chinwalla A, Christoforides A, Cibulskis K, Clark A, Clarke L, Clemm N, Coarfa C, Coffrey A, Conrad D, Cox T, Craig D, Curran M, Daly M, Danecek P, de Bakker P, Degenhardt J, De La Vega F, DePristo M, Dermitzakis M, Ding J, Ding L, Donnelly P, Dooling D, Du J, Durbin J, Durbin R, Eberle M, Eichler E, Fallon V, Fennell T, Flicek P, Freeman C, Fromer M, Fu Y, Fu Y, Gabriel S, Gaffney D, Garimella K, Garrison E, Gerstein M, Gibbs R, Gottipati S, Gravel S, Greer D, Grossman S, Grubert F, Gutenkunst R, Ha G, Habegger L, Haimel M, Hajirasouliha I, Handsaker B, Hanna M, Hansen N, Haraksingh R, Hartl C, Haussler D, Henn B, Hernandez R, Herrero J, Herwig R, Hinrichs A, Homer N, Hormozdiari F, Howie B, Hu M, Huang N, Huang W, Humphray S, Hurles M, Hyland F, Indap A, Iqbal Z, Izatt T, Jaffe D, Jin H, Jones S, Jorde L, Jostins L, Kaganovich M, Kahn S, Kang HM, Kang J, Katzman S, Keane T, Keebler J, Kelley J, Kent J, Keinan A, Kern A, Kernytsky A, Kersey P, Khurana E, Kidd J, Ko A, Koboldt D, Konkel M, Korbel J, Korn J, Kuhn R, Kural D, Kurdoglu A, Lacroute P, Lam H, Lander E, Lappalainen T, Le Q, Lee C, Lee J, Lee J, Lee WP, Leng J, Leong WF, Li B, Li G, Li H, Li L, Li R, Li Y, Li Y, Liang L, Lohmueller K, Long J, Long Q, Lunter G, Ma X, MacArthur D, Maguire J, Majumder P, Makarov V, Marchini J, Mardis E, Marioni J, Marth G, McCarroll S, McCarthy S, McKenna A, McLellan M, Melton C, Merriman B, Mills R, Montgomery S, Moutsianas L, Mu X, Mullikin J, Murray L, Musharoff S, Muzny D, Myers S, Nelson S, Nemesh J, Nickerson E, Nielsen R, Ning Z, Parkhomchuk D, Parkhomenko E, Paschall J, Pearson J, Peckham H, Poplin R, Presgraves D, Pickrell J, Price A, Pritchard J, Przeworski M, Purcell S, Quinlan A, Reid J, Rivas M, Rosenfeld J, Ruiz-Linares A, Sabeti P, Sabo A, Sajjadian S, Sakarya O, Scally A, Schaffner S, Scheet P, Sebat J, Shakir K, Sharpe T, Shaw R, Shefler E, Sherry S, Shi XM, Shlyakhter I, Shumway M, Sinari S, Sivachenko A, Smith R, Snyder M, Snyder M, Sougnez C, Squire K, Stalker J, Stephens M, Stewart C, Stromberg M, Su Y, Sudbrak R, Sudmant P, Sun Y, Taylor P, Thomas D, Tishkoff S, Tsung E, Tyler-Smith C, Urban A, Vincenza C, Wallis J, Walker J, Walter K, Wan Z, Wang J, Wang W, Wang Y, Wang Y, Ward A, Webster T, Weinstock G, Wendl M, Wheeler D, Wong Y, Wu J, Xiao C, Xing J, Xue Y, Yan X, Ye K, Ye K, Yoon S, Yu F, Yu J, Zerbino D, Zhan X, Zhan Y, Zhang K, Zhang Q, Zhang Y, Zhao H, Zhang CK, Zhang Z, Bradley HZ, Zheng W, Zody M, Zoellner S, Flicek P, Sherry S, Abecasis G, Alkan C, Balasubramaniam S, Birney E, Bloom T, Brockington C, Cibulskis K, Clarke L, Cochrane G, Cox T, Craig D, De La Vega F, Dooling D, Fennell T, Gibbs R, Haussler D, Hinrichs A, Humphray S, Iqbal Z, Jamieson R, Kahn S, Katzman S, Keane T, Kent J, Kern A, Ko A, Kuhn R, Li G, Li R, Manning J, McCarthy S, McVean G, Metzker M, Muzny D, Nietfeld W, Paschal J, Peckham H, Reid J, Sajjadian S, Sanders R, Sherry S, Shumway M, Skelly T, Smith R, Stalker J, Sudbrak R, Wang J, Weinstock G, Wilkinson J, Xiao C, Bradley HZ, Amstislavskiy V, Deiros D, Freeman C, McVean G, Przeworski M, Przeworski M, Abecasis G, Arbiza L, Auton A, Ayub Q, Balasubramanian S, Barrett J, Blekham R, Boyko A, Bustamante C, Byrnes J, Chakravarti A, Clark A, Conrad D, Craig D, Dermitzakis M, Durbin R, Fu Y, Gabriel S, Garrison E, Gerstein M, Gottipati S, Gravel S, Grossman S, Gutenkunst R, Habegger L, Handsaker B, Henn B, Hernandez R, Howie B, Hu M, Huang N, Hurles M, Iqbal Z, Indap A, Jin H, Jostins L, Kang J, Katzman S, Keinan A, Kelley J, Khurana E, Kidd J, Lacroute P, Lee J, Leng J, Li B, Li H, Li L, Long Q, Lunter G, MacArthur D, Melton C, Montgomery S, Mu X, Musharoff S, Nielsen R, Presgraves D, Pritchard J, Sabeti P, Shlyakhter I, Snyder M, Tyler-Smith C, Wang W, Zhang CK, Zhang Z, Zhao H, Eichler E, Hurles M, Lee C, Abyzov A, Alkan C, del Angel G, Bafna V, Banks E, Bashir A, Batzer M, Birney E, Blackburne B, Blackwell T, Caccamo M, Cardin N, Cheetham K, Chen K, Chinwalla A, Clarke L, Conrad D, Craig D, Degenhardt J, De La Vega F, DePristo M, Ding L, Fromer M, Fu Y, Garrison E, Gerstein M, Greer D, Grubert F, Ha G, Haimel M, Hajirasouliha I, Handsaker B, Haraksingh R, Hartl C, Homer N, Hormozdiari F, Humphray S, Iqbal Z, Jones S, Kaganovich M, Kahn S, Kersey P, Khurana E, Kidd J, Ko A, Konkel M, Korbel J, Korn J, Kural D, Lacroute P, Lam H, Lee J, Leng J, Li H, Li Y, Lunter G, Marth G, McCarroll S, McLellan M, Mills R, Makarov V, Mu X, Murray L, Nelson S, Nemesh J, Ning Z, Parkhomenko E, Peckham H, Quinlan A, Sajjadian S, Scally A, Sebat J, Shakir K, Shaw R, Snyder M, Snyder M, Stewart C, Stromberg M, Sudmant P, Sun Y, Thomas D, Urban A, Wallis J, Walker J, Walter K, Ward A, Wu J, Xiao C, Xing J, Ye K, Yoon S, Zerbino D, Zhang Y, Zhang Z, Bradley HZ, Gibbs R, Marth G, Abecasis G, Albers K, Bainbridge M, Balasubramaniam S, Balasubramanian S, Blackwell T, Bustamanter C, Challis D, Cibulskis K, Clark A, Clarke L, Coarfa C, Coffrey A, DePristo M, Dermitzakis M, Dooling D, Durbin R, Fennell T, Flicek P, Fulton L, Fulton R, Gabriel S, Garimella K, Garrison E, Gibbs R, Gravel S, Hartl C, Indap A, Iqbal Z, Katzman S, Keane T, Koboldt D, Leong WF, MacArthur D, Mardis E, McVean G, Muzny D, Nickerson E, Palotie A, Paschall J, Reid J, Quinlan A, Sabo A, Shefler E, Sherry S, Shumway M, Smith R, Sougnez C, Stalker J, Sudmant P, Tyler-Smith C, Wang Y, Wang Y, Wilkinson J, Xiao C, Yu F, Bradley HZ, Brooks L, Felsenfeld A, McEwen J, Clemm N, Duncanson A, Dunn M, Eichler E, Guyer M, Hurles M, Hyland F, Jamieson R, Kälin N, Kang L, Laplace F, Lee C, Liu Y, Michelson A, Peterson J, Ren Z, Wang J.

Author information

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.

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

PMID:
21653522
[PubMed - indexed for MEDLINE]
PMCID:
PMC3137218
Free PMC Article

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