DOI: 10.18129/B9.bioc.VariantAnnotation  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.17

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

Author: Bioconductor Package Maintainer [aut, cre], Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]

Maintainer: Bioconductor Package Maintainer <maintainer at>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script 1. Introduction to VariantAnnotation
PDF R Script 2. Using filterVcf to Select Variants from VCF Files
PDF   Reference Manual
Text   NEWS
Video   Reading VCF data


biocViews Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.46.0
In Bioconductor since BioC 2.9 (R-2.14) (12 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), MatrixGenerics, GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.41.5), SummarizedExperiment(>= 1.19.5), Rsamtools(>= 1.99.0)
Imports utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), XVector(>= 0.29.2), Biostrings(>= 2.57.2), AnnotationDbi(>= 1.27.9), rtracklayer(>= 1.39.7), BSgenome(>= 1.47.3), GenomicFeatures(>= 1.31.3)
LinkingTo S4Vectors, IRanges, XVector, Biostrings, Rhtslib(>= 1.99.3)
Suggests RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
SystemRequirements GNU make
Depends On Me alabaster.vcf, annotation, CNVrd2, deepSNV, ensemblVEP, genotypeeval, HelloRanges, HTSeqGenie, myvariant, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, signeR, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CNVfilteR, CopyNumberPlots, COSMIC.67, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, epialleleR, fcScan, GA4GHclient, genbankr, GenomicFiles, GenVisR, ggbio, gmapR, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, MADSEQ, MMAPPR2, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, ProteoDisco, scoreInvHap, SigsPack, SNPhood, svaRetro, TitanCNA, tLOH, TVTB, Uniquorn, VCFArray, YAPSA, ZygosityPredictor
Suggests Me AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CNVgears, CrispRVariants, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, ldblock, omicsPrint, podkat, RVS, SeqArray, splatter, supersigs, systemPipeR, trackViewer, trio, vtpnet
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package VariantAnnotation_1.46.0.tar.gz
Windows Binary
macOS Binary (x86_64) VariantAnnotation_1.46.0.tgz
macOS Binary (arm64) VariantAnnotation_1.46.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: