A global reference for human genetic variation.
Adam Auton,Gonçalo R. Abecasis,David Altshuler,Richard Durbin,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,Peter Donnelly,Evan E. Eichler,Paul Flicek,Stacey Gabriel,Richard A. Gibbs,Eric D. Green,Matthew E. Hurles,Bartha Maria Knoppers,Jan O. Korbel,Eric S. Lander,Charles Lee,Hans Lehrach,Elaine R. Mardis,Gabor T. Marth,Gil McVean,Deborah A. Nickerson,Jeanette Schmidt,Stephen T. Sherry,Jun Wang,Richard K. Wilson,Eric Boerwinkle,Harsha Doddapaneni,Yi Han,Viktoriya Korchina,Christie Kovar,Sandra L. Lee,Donna M. Muzny,Jeffrey G. Reid,Yiming Zhu,Yuqi Chang,Qiang Feng,Qiang Feng,Xiaodong Fang,Xiaodong Fang,Xiaosen Guo,Xiaosen Guo,Min Jian,Min Jian,Hui Jiang,Hui Jiang,Xin Jin,Tianming Lan,Guoqing Li,Jingxiang Li,Yingrui Li,Shengmao Liu,Xiao Liu,Xiao Liu,Yao Lu,Xuedi Ma,Meifang Tang,Bo Wang,Guangbiao Wang,Honglong Wu,Renhua Wu,Xun Xu,Ye Yin,Dandan Zhang,Wenwei Zhang,Jiao Zhao,Meiru Zhao,Xiaole Zheng,Namrata Gupta,Neda Gharani,Lorraine Toji,Norman P. Gerry,Alissa M. Resch,Jonathan Barker,Laura Clarke,Laurent Gil,Sarah E. Hunt,Gavin Kelman,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Asier Roa,Dmitriy Smirnov,Richard Smith,Ian Streeter,Anja Thormann,Iliana Toneva,Brendan Vaughan,Xiangqun Zheng-Bradley,Russell J. Grocock,Sean Humphray,Terena James,Zoya Kingsbury,Ralf Sudbrak,M. Albrecht,Vyacheslav Amstislavskiy,Tatiana A. Borodina,Matthias Lienhard,Florian Mertes,Marc Sultan,Bernd Timmermann,Marie-Laure Yaspo,Lucinda Fulton,Victor Ananiev,Zinaida Belaia,Dimitriy Beloslyudtsev,Nathan Bouk,Chao Chen,Deanna M. Church,Robert M. Cohen,Charles Cook,John Garner,Timothy Hefferon,Mikhail Kimelman,Chunlei Liu,John Lopez,Peter Meric,Chris O’Sullivan,Yuri Ostapchuk,Lon Phan,Sergiy Ponomarov,Valerie A. Schneider,Eugene Shekhtman,Karl Sirotkin,Douglas J. Slotta,Hua Zhang,Senduran Balasubramaniam,John Burton,Petr Danecek,Thomas M. Keane,Anja Kolb-Kokocinski,Shane A. McCarthy,James Stalker,Michael A. Quail,Christopher Davies,Jeremy Gollub,Teresa Webster,Brant Wong,Yiping Zhan,Christopher L. Campbell,Yu Kong,Anthony Marcketta,Fuli Yu,Lilian Antunes,Matthew N. Bainbridge,Aniko Sabo,Zhuoyi Huang,Lachlan J. M. Coin,Lin Fang,Lin Fang,Qibin Li,Zhenyu Li,Haoxiang Lin,Binghang Liu,Ruibang Luo,Haojing Shao,Haojing Shao,Yinlong Xie,Chen Ye,Chang Yu,Fan Zhang,Hancheng Zheng,Zhu Hongmei,Can Alkan,Elif Dal,Fatma Kahveci,Erik Garrison,Deniz Kural,Wan-Ping Lee,Wen Fung Leong,Michael Strömberg,Alistair Ward,Jiantao Wu,Mengyao Zhang,Mark J. Daly,Mark A. DePristo,Robert E. Handsaker,Robert E. Handsaker,Eric Banks,Gaurav Bhatia,Guillermo del Angel,Giulio Genovese,Heng Li,Seva Kashin,Seva Kashin,Steven A. McCarroll,Steven A. McCarroll,James Nemesh,Ryan Poplin,Seungtai Yoon,Jayon Lihm,Vladimir Makarov,Srikanth Gottipati,Alon Keinan,Juan L. Rodriguez-Flores,Tobias Rausch,Markus Hsi-Yang Fritz,Adrian M. Stütz,Kathryn Beal,Avik Datta,Javier Herrero,Graham R. S. Ritchie,Daniel R. Zerbino,Pardis C. Sabeti,Pardis C. Sabeti,Ilya Shlyakhter,Ilya Shlyakhter,Stephen F. Schaffner,Stephen F. Schaffner,Joseph J. Vitti,Joseph J. Vitti,David Neil Cooper,Edward V. Ball,Peter D. Stenson,Bret Barnes,Markus J. Bauer,R. Keira Cheetham,Anthony J. Cox,Michael A. Eberle,Scott Kahn,Lisa Murray,John F. Peden,Richard Shaw,Eimear E. Kenny,Mark A. Batzer,Miriam K. Konkel,Jerilyn A. Walker,Daniel G. MacArthur,Monkol Lek,Ralf Herwig,Li Ding,Daniel C. Koboldt,David E. Larson,Kai Ye,Simon Gravel,Anand Swaroop,Emily Y. Chew,Tuuli Lappalainen,Yaniv Erlich,Melissa Gymrek,Melissa Gymrek,Thomas Willems,Jared T. Simpson,Mark D. Shriver,Jeffrey A. Rosenfeld,Carlos Bustamante,Stephen B. Montgomery,Francisco M. De La Vega,Jake K. Byrnes,Andrew Carroll,Marianne K. DeGorter,Phil Lacroute,Brian K. Maples,Alicia R. Martin,Andrés Moreno-Estrada,Andrés Moreno-Estrada,Suyash Shringarpure,Fouad Zakharia,Eran Halperin,Eran Halperin,Yael Baran,Eliza Cerveira,Jaeho Hwang,Ankit Malhotra,Dariusz Plewczynski,Kamen Radew,Mallory Romanovitch,Chengsheng Zhang,Fiona Hyland,David Craig,Alexis Christoforides,Nils Homer,Tyler Izatt,Ahmet Kurdoglu,Shripad Sinari,Kevin Squire,Chunlin Xiao,Jonathan Sebat,Danny Antaki,Madhusudan Gujral,Amina Noor,Kenny Ye,Esteban G. Burchard,Ryan D. Hernandez,Christopher R. Gignoux,David Haussler,David Haussler,Sol Katzman,W. James Kent,Bryan Howie,Andres Ruiz-Linares,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Scott E. Devine,Hyun Min Kang,Jeffrey M. Kidd,Thomas W. Blackwell,Sean Caron,Wei Chen,S. Emery,Lars G. Fritsche,Christian Fuchsberger,Goo Jun,Goo Jun,Bingshan Li,Robert H. Lyons,Chris Scheller,Carlo Sidore,Carlo Sidore,Carlo Sidore,Shiya Song,Elzbieta Sliwerska,Daniel Taliun,Adrian Tan,Ryan P. Welch,Mary Kate Wing,Xiaowei Zhan,Philip Awadalla,Philip Awadalla,Alan Hodgkinson,Yun Li,Xinghua Shi,Andrew Quitadamo,Gerton Lunter,Jonathan Marchini,Simon Myers,Claire Churchhouse,Olivier Delaneau,Olivier Delaneau,Anjali Gupta-Hinch,Warren W. Kretzschmar,Zamin Iqbal,Iain Mathieson,Androniki Menelaou,Androniki Menelaou,Andy Rimmer,Dionysia Kiara Xifara,Taras K. Oleksyk,Yunxin Fu,Xiaoming Liu,Momiao Xiong,Lynn B. Jorde,David J. Witherspoon,Jinchuan Xing,Brian L. Browning,Sharon R. Browning,Fereydoun Hormozdiari,Peter H. Sudmant,Ekta Khurana,Chris Tyler-Smith,Cornelis A. Albers,Qasim Ayub,Yuan Chen,Vincenza Colonna,Vincenza Colonna,Luke Jostins,Klaudia Walter,Yali Xue,Mark Gerstein,Alexej Abyzov,Suganthi Balasubramanian,Jieming Chen,Declan Clarke,Yao Fu,Arif Harmanci,Mike Jin,Dong-Hoon Lee,Jeremy Liu,Xinmeng Jasmine Mu,Xinmeng Jasmine Mu,Jing Zhang,Yan Zhang,Christopher Hartl,Khalid Shakir,Jeremiah D. Degenhardt,Sascha Meiers,Benjamin Raeder,Francesco Paolo Casale,Oliver Stegle,Eric-Wubbo Lameijer,Ira M. Hall,Vineet Bafna,Jacob J. Michaelson,Eugene J. Gardner,Ryan E. Mills,Gargi Dayama,Ken Chen,Xian Fan,Zechen Chong,Tenghui Chen,Mark Chaisson,John Huddleston,Maika Malig,Bradley J. Nelson,Nicholas F. Parrish,Ben Blackburne,Sarah J. Lindsay,Zemin Ning,Yujun Zhang,Hugo Y. K. Lam,Cristina Sisu,Danny Challis,Uday S. Evani,James T. Lu,Uma Nagaswamy,Jin Yu,Wangshen Li,Lukas Habegger,Haiyuan Yu,Fiona Cunningham,Ian Dunham,Kasper Lage,Kasper Lage,Jakob Berg Jespersen,Jakob Berg Jespersen,Jakob Berg Jespersen,Heiko Horn,Heiko Horn,Donghoon Kim,Rob DeSalle,Apurva Narechania,Melissa A. Wilson Sayres,Fernando L. Mendez,G. David Poznik,Peter A. Underhill,David Mittelman,Ruby Banerjee,Maria Cerezo,Thomas W. Fitzgerald,Sandra Louzada,Andrea Massaia,Fengtang Yang,Divya Kalra,Walker Hale,Xu Dan,Kathleen C. Barnes,Christine Beiswanger,Hongyu Cai,Hongzhi Cao,Hongzhi Cao,Brenna M. Henn,Danielle Jones,Jane Kaye,Alastair Kent,Angeliki Kerasidou,Rasika A. Mathias,Pilar N. Ossorio,Michael Parker,Charles N. Rotimi,Charmaine D.M. Royal,Karla Sandoval,Yeyang Su,Zhongming Tian,Sarah A. Tishkoff,Marc Via,Yuhong Wang,Huanming Yang,Ling Yang,Jiayong Zhu,Walter F. Bodmer,Gabriel Bedoya,Zhiming Cai,Yang Gao,Jiayou Chu,Leena Peltonen,Andrés C. García-Montero,Alberto Orfao,Julie Dutil,Juan Carlos Martínez-Cruzado,R. Mathias,Anselm Hennis,Harold Watson,Colin A. McKenzie,Firdausi Qadri,Regina C. LaRocque,Xiaoyan Deng,Danny Asogun,Onikepe A. Folarin,Christian T. Happi,Omonwunmi Omoniwa,Matt Stremlau,Matt Stremlau,Ridhi Tariyal,Ridhi Tariyal,M Jallow,M Jallow,Fatoumatta Sisay Joof,Fatoumatta Sisay Joof,Tumani Corrah,Tumani Corrah,Kirk A. Rockett,Kirk A. Rockett,Dominic P. Kwiatkowski,Dominic P. Kwiatkowski,Jaspal S. Kooner,Tran Tinh Hien,Sarah J. Dunstan,Sarah J. Dunstan,Nguyen ThuyHang,Richard Fonnie,Robert F. Garry,Lansana Kanneh,Lina M. Moses,John S. Schieffelin,Donald S. Grant,Carla Gallo,Giovanni Poletti,Danish Saleheen,Asif Rasheed,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Yekaterina Vaydylevich,Audrey Duncanson,Michael Dunn,Jeffery A. Schloss +517 more
TLDR
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.Abstract:
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.read more
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Benefits and limitations of genome-wide association studies.
Vivian W.Y. Tam,Nikunj Patel,Michelle Turcotte,Yohan Bossé,Guillaume Paré,David Meyre,David Meyre +6 more
TL;DR: This Review comprehensively assess the benefits and limitations of GWAS in human populations and discusses the relevance of performing more GWAS, with a focus on the cardiometabolic field.
Journal ArticleDOI
The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease
William J. Astle,Heather Elding,Heather Elding,Tao Jiang,Dave Allen,Dace Ruklisa,Dace Ruklisa,Alice L. Mann,Daniel Mead,Heleen J. Bouman,Fernando Riveros-Mckay,Myrto Kostadima,Myrto Kostadima,Myrto Kostadima,John J. Lambourne,John J. Lambourne,Suthesh Sivapalaratnam,Suthesh Sivapalaratnam,Kate Downes,Kate Downes,Kousik Kundu,Kousik Kundu,Lorenzo Bomba,Kim Berentsen,John Bradley,John Bradley,Louise C. Daugherty,Louise C. Daugherty,Olivier Delaneau,Kathleen Freson,Stephen F. Garner,Stephen F. Garner,Luigi Grassi,Luigi Grassi,Jose A. Guerrero,Jose A. Guerrero,Matthias Haimel,Eva M. Janssen-Megens,Anita Kaan,Mihir A Kamat,Bowon Kim,Amit Mandoli,Jonathan Marchini,Jonathan Marchini,Joost H.A. Martens,Stuart Meacham,Stuart Meacham,Karyn Megy,Karyn Megy,Jared O'Connell,Jared O'Connell,Romina Petersen,Romina Petersen,Nilofar Sharifi,S.M. Sheard,James R Staley,Salih Tuna,Martijn van der Ent,Klaudia Walter,Shuang-Yin Wang,Eleanor Wheeler,Steven P. Wilder,Valentina Iotchkova,Valentina Iotchkova,Carmel Moore,Jennifer G. Sambrook,Jennifer G. Sambrook,Hendrik G. Stunnenberg,Emanuele Di Angelantonio,Emanuele Di Angelantonio,Emanuele Di Angelantonio,Stephen Kaptoge,Stephen Kaptoge,Taco W. Kuijpers,Enrique Carrillo-de-Santa-Pau,David Juan,Daniel Rico,Alfonso Valencia,Lu Chen,Lu Chen,Bing Ge,Louella Vasquez,Tony Kwan,Diego Garrido-Martín,Stephen Watt,Ying Yang,Roderic Guigó,Stephan Beck,Dirk S. Paul,Dirk S. Paul,Tomi Pastinen,David Bujold,Guillaume Bourque,Mattia Frontini,Mattia Frontini,Mattia Frontini,John Danesh,David J. Roberts,David J. Roberts,Willem H. Ouwehand,Adam S. Butterworth,Adam S. Butterworth,Adam S. Butterworth,Nicole Soranzo +103 more
TL;DR: A genome-wide association analysis in the UK Biobank and INTERVAL studies is performed, providing evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations betweenBlood cell indices and cardiovascular disease may be non-causal.
Journal ArticleDOI
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
Carlos Alonso-Blanco,Jorge Andrade,Claude Becker,Felix Bemm,Joy Bergelson,Karsten M. Borgwardt,Jun Cao,Eunyoung Chae,Todd M. Dezwaan,Wei Ding,Joseph R. Ecker,Moises Exposito-Alonso,Ashley Farlow,Joffrey Fitz,Xiangchao Gan,Dominik G. Grimm,Angela M. Hancock,Stefan R. Henz,Svante Holm,Matthew W. Horton,Mike Jarsulic,Randall A. Kerstetter,Arthur Korte,Pamela Korte,Christa Lanz,Cheng-Ruei Lee,Dazhe Meng,Todd P. Michael,Richard Mott,Ni Wayan Muliyati,Thomas Nägele,Matthias Nagler,Viktoria Nizhynska,Magnus Nordborg,Polina Yu. Novikova,F. Xavier Picó,Alexander Platzer,Fernando A. Rabanal,Alex Rodriguez,Beth A. Rowan,Patrice A. Salomé,Karl Schmid,Robert J. Schmitz,Ümit Seren,Felice Gianluca Sperone,Mitchell Sudkamp,Hannes Svardal,Matt M. Tanzer,Donald Todd,Samuel L. Volchenboum,Congmao Wang,George Wang,Xi Wang,Wolfram Weckwerth,Detlef Weigel,Xuefeng Zhou +55 more
TL;DR: Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
Journal ArticleDOI
The landscape of genomic alterations across childhood cancers
Susanne Gröbner,Barbara C. Worst,Joachim Weischenfeldt,Joachim Weischenfeldt,Ivo Buchhalter,Kortine Kleinheinz,Vasilisa A. Rudneva,Pascal Johann,Gnana Prakash Balasubramanian,Maia Segura-Wang,Sebastian Brabetz,Sebastian Bender,Barbara Hutter,Dominik Sturm,Elke Pfaff,Daniel Hübschmann,Gideon Zipprich,Michael Heinold,Michael Heinold,Jürgen Eils,Christian Lawerenz,Serap Erkek,Sander Lambo,Sebastian M. Waszak,Claudia Blattmann,Arndt Borkhardt,Arndt Borkhardt,Michaela Kuhlen,Michaela Kuhlen,Angelika Eggert,Angelika Eggert,Simone Fulda,Manfred Gessler,Jenny Wegert,Roland Kappler,Roland Kappler,Daniel Baumhoer,Stefan Burdach,Stefan Burdach,Renate Kirschner-Schwabe,Renate Kirschner-Schwabe,Udo Kontny,Andreas E. Kulozik,Andreas E. Kulozik,Dietmar R. Lohmann,Simone Hettmer,Cornelia Eckert,Cornelia Eckert,Stefan S. Bielack,Michaela Nathrath,Michaela Nathrath,Charlotte M. Niemeyer,Charlotte M. Niemeyer,Gunther Richter,Gunther Richter,Johannes H. Schulte,Johannes H. Schulte,Reiner Siebert,Frank Westermann,Jan J. Molenaar,Gilles Vassal,Hendrik Witt,Peter Lichter,Ursula Weber,Roland Eils,Roland Eils,Andrey Korshunov,Olaf Witt,Stefan Pfister,Guido Reifenberger,J Felsberg,Christof von Kalle,Manfred Schmidt,Cynthia Bartholomä,Michael Taylor,David T. W. Jones,Natalie Jäger,Korbel Jo,Adrian M. Stütz,Tobias Rausch,Bernhard Radlwimmer,Marie-Laure Yaspo,Hans Lehrach,Hans-Jörg Warnatz,Pablo Landgraf,Benedikt Brors,Marc Zapatka,Marc Zapatka,Susanne Wagner,Susanne Wagner,Andrea Haake,Julia Richter,Gesine Richter,Gesine Richter,Chris Lawerenz,Jules Kerssemakers,Christina Jaeger-Schmidt,Ingrid Scholz,Anke K. Bergmann,Christoph Borst,Birgit Burkhardt,Alexander Claviez,Martin Dreyling,Martin Dreyling,Sonja Eberth,Hermann Einsele,Norbert Frickhofen,Siegfried Haas,Martin-Leo Hansmann,Dennis Karsch,Michael Kneba,Jasmin Lisfeld,Luisa Mantovani-Löffler,Marius Rohde,German Ott,Christina Stadler,Peter Staib,Stephan Stilgenbauer,Lorenz Trümper,Thorsten Zenz,Dieter Kube,Ralf Küppers,Marc A. Weniger,Michael Hummel,Wolfram Klapper,Ulrike Kostezka,Dido Lenze,Peter Möller,Andreas Rosenwald,Monika Szczepanowski,Ole Ammerpohl,Sietse M. Aukema,Vera Binder,Jessica I. Hoell,Ellen Leich,Cristina López,Inga Nagel,Jordan Pischimariov,Philip Rosenstiel,Markus Schilhabel,Stefan Schreiber,Inga Vater,Rabea Wagener,Stephan H. Bernhart,Hans Binder,Gero Doose,Steve Hoffmann,Lydia Hopp,Helene Kretzmer,Markus Kreuz,David Langenberger,Markus Loeffler,Maciej Rosolowski,Matthias Schlesner,Peter F. Stadler,Stephanie Sungalee,Christian P. Kratz,Cornelis M. van Tilburg,Christof M. Kramm,Gudrun Fleischhack,Gudrun Fleischhack,Uta Dirksen,Stefan Rutkowski,Michael C. Frühwald,Katja von Hoff,Stephan Wolf,Thomas Klingebiel,Thomas Klingebiel,Ewa Koscielniak,Jan Koster,Adam C. Resnick,Jinghui Zhang,Yanling Liu,Xin Zhou,Angela J. Waanders,Danny A. Zwijnenburg,Pichai Raman,Ursula D. Weber,Paul A. Northcott,Kristian W. Pajtler,Marcel Kool,Rosario M. Piro,Jan O. Korbel,David T.W. Jones,Lukas Chavez,Stefan M. Pfister +185 more
TL;DR: The data suggest that 7–8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
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Universal Patterns of Selection in Cancer and Somatic Tissues
Inigo Martincorena,Keiran Raine,Moritz Gerstung,Kevin J. Dawson,Kerstin Haase,Peter Van Loo,Peter Van Loo,Helen Davies,Michael R. Stratton,Peter J. Campbell,Peter J. Campbell +10 more
TL;DR: This work adapted methods from molecular evolution and applied them to 7,664 tumors across 29 cancer types, allowing exome-wide enumeration of all driver coding mutations, including outside known cancer genes.
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