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Bioinformatics. 2014 Jul 15;30(14):2076-8. doi: 10.1093/bioinformatics/btu168. Epub 2014 Mar 28.

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.

Author information

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

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.

PMID:
24681907
PMCID:
PMC4080743
DOI:
10.1093/bioinformatics/btu168
[Indexed for MEDLINE]
Free PMC Article

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