title: VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.
abstract: 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.
  
  
  METHODS
  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.affiliation: 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.
authors.forename: Valerie
authors.initials: V
authors.lastname: Obenchain
authors.affiliation: 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.
authors.forename: Michael
authors.initials: M
authors.lastname: Lawrence
authors.affiliation: 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.
authors.forename: Vincent
authors.initials: V
authors.lastname: Carey
authors.affiliation: 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.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Gogarten
authors.affiliation: 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.
authors.forename: Paul
authors.initials: P
authors.lastname: Shannon
authors.affiliation: 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.
authors.forename: Martin
authors.initials: M
authors.lastname: Morgan
mesh_terms: D014644:Genetic Variation; D023281:Genomics; D058977:Molecular Sequence Annotation; D012984:Software