Annotation of Genetic Variants

Bioconductor version: Development (3.0)

Annotate variants, compute amino acid coding changes, predict coding outcomes

Author: Valerie Obenchain, Martin Morgan, Michael Lawrence with contributions from Stephanie Gogarten.

Maintainer: Valerie Obenchain <vobencha at>

To install this package, start R and enter:


Citation (from within R, enter citation("VariantAnnotation")):


PDF R Script filterVcf Overview
PDF R Script Introduction to VariantAnnotation
PDF   Reference Manual
Text   NEWS


biocViews Annotation, DataImport, Genetics, SNP, Sequencing, Software
Version 1.11.16
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.7.7), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.23), Rsamtools(>= 1.17.26)
Imports utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.0.6), IRanges(>= 1.99.21), XVector(>= 0.5.6), Biostrings(>= 2.33.5), AnnotationDbi(>= 1.27.1), BSgenome, rtracklayer(>= 1.25.5), GenomicFeatures(>= 1.17.5)
Suggests RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
System Requirements
Depends On Me ampliQueso, cgdv17, CNVrd2, deepSNV, ensemblVEP, HTSeqGenie, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, VariantTools
Imports Me biovizBase, COSMIC.67, customProDB, FunciSNP, ggbio, GGtools, gmapR, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, R453Plus1Toolbox, Rariant, SeqArray, SomaticSignatures, VariantFiltering
Suggests Me GenomicRanges, GWASTools, trio, vtpnet

Package Downloads

Package Source VariantAnnotation_1.11.16.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VariantAnnotation_1.11.16.tgz
Mac OS X 10.9 (Mavericks) VariantAnnotation_1.11.16.tgz
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