<tt>VariantAnnotation</tt> : a <tt>Bioconductor</tt> package for exploration and annotation of genetic variants

TLDR

VariantAnnotation is an R/Bioconductor package that enables exploration and annotation of genetic variants by reading, writing, and filtering VCF files and integrating with other R/Bioconductor tools for advanced analysis, transformation, visualization, and genomic resource integration. The package is implemented in R, available from Bioconductor, includes extensive help pages and a vignette, and is released under the Artistic‑2.0 license (version 1.9.38). Contact: [e-mail].

Abstract

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: [e-mail]