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

2014; Oxford University Press; Volume: 30; Issue: 14 Linguagem: Inglês

10.1093/bioinformatics/btu168

1367-4811

Valerie Obenchain, Michael Lawrence, Vincent J. Carey, Stephanie M. Gogarten, Paul Shannon, Martin Morgan,

Bioinformatics and Genomic Networks

Abstract Summary: 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. Contact: vobencha@fhcrc.org