Valerie Obenchain1, Michael Lawrence1, Vincent Carey1, Stephanie Gogarten1, Paul Shannon1, Martin Morgan1. 1. Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 and Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
Abstract
UNLABELLED: VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing and filtering variant call format (VCF) files. VariantAnnotation allows ready access to additional R / Bioconductor facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. AVAILABILITY AND IMPLEMENTATION: This package is implemented in R and available for download at the Bioconductor Web site (http://bioconductor.org/packages/2.13/bioc/html/VariantAnnotation.html). The package contains extensive help pages for individual functions and a 'vignette' outlining typical work flows; it is made available under the open source 'Artistic-2.0' license. Version 1.9.38 was used in this article.
UNLABELLED: VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing and filtering variant call format (VCF) files. VariantAnnotation allows ready access to additional R / Bioconductor facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. AVAILABILITY AND IMPLEMENTATION: This package is implemented in R and available for download at the Bioconductor Web site (http://bioconductor.org/packages/2.13/bioc/html/VariantAnnotation.html). The package contains extensive help pages for individual functions and a 'vignette' outlining typical work flows; it is made available under the open source 'Artistic-2.0' license. Version 1.9.38 was used in this article.
Authors: Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo Journal: Genome Res Date: 2010-07-19 Impact factor: 9.043
Authors: Daniel C Koboldt; Qunyuan Zhang; David E Larson; Dong Shen; Michael D McLellan; Ling Lin; Christopher A Miller; Elaine R Mardis; Li Ding; Richard K Wilson Journal: Genome Res Date: 2012-02-02 Impact factor: 9.043
Authors: Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang Journal: Genome Biol Date: 2004-09-15 Impact factor: 13.583
Authors: Radoje Drmanac; Andrew B Sparks; Matthew J Callow; Aaron L Halpern; Norman L Burns; Bahram G Kermani; Paolo Carnevali; Igor Nazarenko; Geoffrey B Nilsen; George Yeung; Fredrik Dahl; Andres Fernandez; Bryan Staker; Krishna P Pant; Jonathan Baccash; Adam P Borcherding; Anushka Brownley; Ryan Cedeno; Linsu Chen; Dan Chernikoff; Alex Cheung; Razvan Chirita; Benjamin Curson; Jessica C Ebert; Coleen R Hacker; Robert Hartlage; Brian Hauser; Steve Huang; Yuan Jiang; Vitali Karpinchyk; Mark Koenig; Calvin Kong; Tom Landers; Catherine Le; Jia Liu; Celeste E McBride; Matt Morenzoni; Robert E Morey; Karl Mutch; Helena Perazich; Kimberly Perry; Brock A Peters; Joe Peterson; Charit L Pethiyagoda; Kaliprasad Pothuraju; Claudia Richter; Abraham M Rosenbaum; Shaunak Roy; Jay Shafto; Uladzislau Sharanhovich; Karen W Shannon; Conrad G Sheppy; Michel Sun; Joseph V Thakuria; Anne Tran; Dylan Vu; Alexander Wait Zaranek; Xiaodi Wu; Snezana Drmanac; Arnold R Oliphant; William C Banyai; Bruce Martin; Dennis G Ballinger; George M Church; Clifford A Reid Journal: Science Date: 2009-11-05 Impact factor: 47.728
Authors: Michael Lawrence; Wolfgang Huber; Hervé Pagès; Patrick Aboyoun; Marc Carlson; Robert Gentleman; Martin T Morgan; Vincent J Carey Journal: PLoS Comput Biol Date: 2013-08-08 Impact factor: 4.475
Authors: 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 Journal: Bioinformatics Date: 2011-06-07 Impact factor: 6.937
Authors: Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean Journal: Nature Date: 2012-11-01 Impact factor: 49.962
Authors: Manuel Giollo; David T Jones; Marco Carraro; Emanuela Leonardi; Carlo Ferrari; Silvio C E Tosatto Journal: Hum Mutat Date: 2017-03-21 Impact factor: 4.878
Authors: Wolfgang Huber; Vincent J Carey; Robert Gentleman; Simon Anders; Marc Carlson; Benilton S Carvalho; Hector Corrada Bravo; Sean Davis; Laurent Gatto; Thomas Girke; Raphael Gottardo; Florian Hahne; Kasper D Hansen; Rafael A Irizarry; Michael Lawrence; Michael I Love; James MacDonald; Valerie Obenchain; Andrzej K Oleś; Hervé Pagès; Alejandro Reyes; Paul Shannon; Gordon K Smyth; Dan Tenenbaum; Levi Waldron; Martin Morgan Journal: Nat Methods Date: 2015-02 Impact factor: 28.547
Authors: Alexandre Kuhn; Yao Min Ong; Ching-Yu Cheng; Tien Yin Wong; Stephen R Quake; William F Burkholder Journal: Proc Natl Acad Sci U S A Date: 2014-05-20 Impact factor: 11.205
Authors: Eveline E Vietsch; Garrett T Graham; Justine N McCutcheon; Aamir Javaid; Giuseppe Giaccone; John L Marshall; Anton Wellstein Journal: Cancer Genet Date: 2017-09-14
Authors: Zichen Wang; Li Li; Benjamin S Glicksberg; Ariel Israel; Joel T Dudley; Avi Ma'ayan Journal: J Biomed Inform Date: 2017-11-04 Impact factor: 6.317