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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Warwick Daw,Frauke Degenhard,Graciela E. Delgado,Alessandro P Delitala,Ayse Demirkan,Xuan Deng,Poornima Devineni,Alexander Dietl,Maria Dimitriou,Latchezar Dimitrov,Rajkumar Dorajoo,Arif B. Ekici,Jorgen Engmann,Zammy Fairhurst-Hunter,Aliki-Eleni Farmaki,Jessica D. Faul,Juan Carlos Fernández-López,Lukas Forer,Margherita Francescatto,Sandra Freitag-Wolf,Christian Fuchsberger,Tessel E. Galesloot,Yan Gao,Zishan Gao,Frank Geller,Olga Giannakopoulou,Franco Giulianini,Anette P. Gjesing,Anuj Goel,Scott D. Gordon,Mathias Gorski,Sarah E. Graham,Jakob Grove,Xiuqing Guo,Stefan Gustafsson,Jeffrey Haessler,Thomas Hansen,Aki S. Havulinna,Simon Haworth,Jiang He,Nancy L. Heard-Costa,Prashantha Hebbar,George Hindy,Yuk-Lam Ho,Edith Hofer,Elizabeth G. Holliday,Katrin Horn,Whitney E. Hornsby,Jouke-Jan Hottenga,Hongyan Huang,Jie Huang,Alicia Huerta-Chagoya,Jennifer E. Huffman,Yi Jen Hung,Shaofeng Huo,Mi Yeong Hwang,H. Iha,Daisuke Ikeda,Masato Isono,Anne U. Jackson,Susanne Jäger,Iris E. 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Timmers,Stella Trompet,Constance Turman,Simona Vaccargiu,Sander W. van der Laan,Peter J. van der Most,Jan B. van Klinken,Jessica van Setten,Shefali S. Verma,Niek Verweij,Yogasudha Veturi,Carol A. Wang,Chaolong Wang,Lihua Wang,Zhe Wang,Helen R. Warren,Wenjie Wei,Ananda R. Wickremasinghe,Matthias Wielscher,Kerri L. Wiggins,Bendik S. Winsvold,Andrew Wong,Yang Wu,Matthias Wuttke,Rong Xi,Tian Xie,Ken Yamamoto,Jingyun Yang,Jie Yao,Hannah Young,Noha A. Yousri,Lingyao Zeng,Weihua Zhang,Xinyuan Zhang,Jing Hua Zhao,Wei Zhao,Wei Zhou,Martina E. Zimmermann,Magdalena Zoledziewska,Linda S. Adair,Hieab H.H. Adams,Carlos A. Aguilar-Salinas,Fahd Al-Mulla,Donna K. Arnett,Folkert W. Asselbergs,Bjørn Olav Åsvold,John Attia,Bernhard Banas,Stefania Bandinelli,David A. Bennett,Tobias Bergler,Dwaipayan Bharadwaj,Ginevra Biino,Hans Bisgaard,Eric Boerwinkle,Carsten A. Böger,Klaus Bønnelykke,Dorret I. Boomsma,Anders D. Børglum,Judith B. Borja,Claude Bouchard,Donald W. Bowden,Ivan Brandslund,Ben Michael Brumpton,Julie E. Buring,Mark J. Caulfield,John C. Chambers,Giriraj R. Chandak,Stephen J. Chanock,Nish Chaturvedi,Yii-Der Ida Chen,Zhengming Chen,Ching-Yu Cheng,Ingrid E. Christophersen,Marina Ciullo,John W. Cole,Francis S. Collins,Richard S. Cooper,Miguel Cruz,Francesco Cucca,L. Adrienne Cupples,Michael J. Cutler,Scott M. Damrauer,Thomas Meinertz Dantoft,Gert J. de Borst,Lisette C. P. G. M. de Groot,Philip L. De Jager,Dominique P.V. de Kleijn,H. Janaka de Silva,George Dedoussis,Anneke I. den Hollander,Shufa Du,Douglas F. Easton,Petra J. M. Elders,A. Heather Eliassen,Patrick T. Ellinor,Sölve Elmståhl,Jeanette Erdmann,Michele K. Evans,Diane Fatkin,Bjarke Feenstra,Mary F. Feitosa,Luigi Ferrucci,Ian Ford,Myriam Fornage,Andre Franke,Paul W. Franks,Barry I. Freedman,Paolo Gasparini,Christian Gieger,Giorgia Girotto,Michael E. Goddard,Yvonne M. Golightly,Clicerio González-Villalpando,Penny Gordon-Larsen,Harald Grallert,Struan F.A. Grant,Niels Grarup,Lyn R. Griffiths,Leif Groop,Vilmundur Gudnason,Christopher A. Haiman,Hakon Hakonarson,Torben Hansen,Catharina A. Hartman,Andrew T. Hattersley,Caroline Hayward,Susan R. Heckbert,Chew-Kiat Heng,Christian Hengstenberg,Alex W. Hewitt,Haretsugu Hishigaki,Carel B. Hoyng,Paul L. Huang,Wei Huang,Steven C. Hunt,Kristian Hveem,Elina Hyppönen,William G. Iacono,Sahoko Ichihara,M. Arfan Ikram,Carmen R. Isasi,Rebecca D. Jackson,Marjo-Ritta Jarvelin,Zidan Jin,Karl-Heinz Jöckel,Peter K. Joshi,Pekka Jousilahti,J. Wouter Jukema,Mika Kähönen,Yoichiro Kamatani,Kui Dong Kang,Jaakko Kaprio,Sharon L.R. Kardia,Fredrik Karpe,Norihiro Kato,Frank Kee,Thorsten Kessler,Amit Khera,Chiea Chuen Khor,Lambertus A. Kiemeney,Bong-Jo Kim,EunGyul Kim,Hyung Lae Kim,Paulus Kirchhof,M Kivimaki,Woon-Puay Koh,Heikki A. Koistinen,Genovefa Kolovou,Jaspal S. Kooner,Charles Kooperberg,Anna Köttgen,Peter Kovacs,Adriaan O. Kraaijeveld,Peter Kraft,R. Krauß,Meena Kumari,Zoltán Kutalik,Markku Laakso,Leslie A. Lange,Claudia Langenberg,Lenore J. Launer,Loic Le Marchand,Hye Jin Lee,Nanette R. Lee,Terho Lehtimäki,Huaixing Li,Liming Li,Wolfgang Liebig,Xu(林旭) Lin,Lars Lind,Allan Linneberg,Ching-Ti Liu,Jianjun Liu,Markus Loeffler,Barry London,Steven A. Lubitz,Stephen J. Lye,David A. Mackey,Reedik Mägi,Patrik K. E. Magnusson,Gregory M. Marcus,Pedro Marques Vidal,Nicholas G. Martin,Winfried März,Fumihiko Matsuda,Robert W. McGarrah,Matt McGue,Amy Jayne McKnight,Sarah E. Medland,Dan Mellström,Andres Metspalu,Braxton D. Mitchell,Paul Mitchell,Dennis O. Mook-Kanamori,Andrew D. Morris,Lorelei A. Mucci,Patricia B. Munroe,Mike A. Nalls,Saman Nazarian,Amanda E. Nelson,Matt Neville,Christopher Newton-Cheh,Christopher Sivert Nielsen,Markus M. Nöthen,Claes Ohlsson,Albertine J. Oldehinkel,Lorena Orozco,Katja Pahkala,Päivi Pajukanta,Colin N. A. Palmer,Esteban J. Parra,Cristian Pattaro,Oluf Pedersen,Craig E. Pennell,Brenda W.J.H. Penninx,Louis Pérusse,Annette Peters,Patricia A. Peyser,David J. Porteous,Danielle Posthuma,Chris Power,Peter P. Pramstaller,Michael A. Province,Qibin Qi,Jia Qu,Daniel J. Rader,Olli T. Raitakari,Sarju Ralhan,Loukianos S. Rallidis,Dabeeru C. Rao,Susan Redline,Dermot F. Reilly,Alexander P. Reiner,Sang Youl Rhee,Paul M. Ridker,Michiel Rienstra,Samuli Ripatti,Marylyn D. Ritchie,Dan M. Roden,Frits R. Rosendaal,Jerome I. Rotter,Igor Rudan,Femke Rutters,Charumathi Sabanayagam,Danish Saleheen,Veikko Salomaa,Nilesh J. Samani,Dharambir K. Sanghera,Naveed Sattar,Börge Schmidt,E. E. Schmidt,Reinhold Schmidt,Matthias B. Schulze,Heribert Schunkert,Laura J. Scott,Rodney J. Scott,Peter S. Sever,Eric J. Shiroma,M. Benjamin Shoemaker,Xiao-Ou Shu,Eleanor M. Simonsick,Mario Sims,Jai Rup Singh,Andrew B. Singleton,Moritz F. Sinner,J. Gustav Smith,Harold Snieder,Tim D. Spector,Meir J. Stampfer,Klaus Stark,David P. Strachan,Leen M 't Hart,Yasuharu Tabara,Hua Tang,Jean-Claude Tardif,Thangavel Alphonse Thanaraj,Nicholas J. Timpson,Anke Tönjes,Angelo Tremblay,Tiinamaija Tuomi,Jaakko Tuomilehto,María Teresa Tusié-Luna,André G. Uitterlinden,Rob M. van Dam,P. Van der Harst,Nathalie van der Velde,Cornelia M. van Duijn,Natasja M. van Schoor,Veronique Vitart,Uwe Völker,Peter Vollenweider,Henry Völzke,Scott I. Vrieze,Niels Wacher-Rodarte,Mark Walker,Ya Xing Wang,Nicholas J. Wareham,Richard M. Watanabe,Hugh Watkins,David R. Weir,Thomas Werge,Elisabeth Widen,Lynne R. Wilkens,Gonneke Willemsen,Walter C. Willett,James F. Wilson,Tien Yin Wong,Jeong Taek Woo,Alan F. Wright,Jer-Yuarn Wu,Huichun Xu,Chittaranjan S. Yajnik,Mitsuhiro Yokota,Jian-Min Yuan,Eleftheria Zeggini,Babette S. Zemel,Wei Zheng,Xiaofeng Zhu,Joseph M. Zmuda,Alan B. Zonderman,John-Anker Zwart,Daniel I. Chasman,Yoon Shin Cho,Iris M. Heid,Mark I. McCarthy,Maggie C.Y. Ng,Christopher J. O'Donnell,Fernando Rivadeneira,Unnur Thorsteinsdottir,Yan V. Sun,E. Shyong Tai,Michael Boehnke,Panos Deloukas,Anne E. Justice,Cecilia M. Lindgren,Ruth J. F. Loos,Karen L. Mohlke,Kari E. North,Kari Stefansson,Robin G. Walters,Thomas W. Winkler,Kristin L. Young,Po-ru Loh,Tõnu Esko,Themistocles L. Assimes,Adam Auton,Gonçalo R. Abecasis,Cristen J. Willer,Adam E. Locke,Sonja I. Berndt,Guillaume Lettre,Timothy M. Frayling,Yukinori Okada,Andrew R. Wood,Peter M. Visscher,Joel N. Hirschhorn +617 more
TL;DR: In this article , the authors show that common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.