VariantAnnotation
This is the released version of VariantAnnotation; for the devel version, see VariantAnnotation.
All Bioconductor versions of VariantAnnotation
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9
Annotation of Genetic Variants
Bioconductor version: 3.23 · Package version: 1.58.0
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Author: Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb], Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation
From within R, enter citation("VariantAnnotation"):
Valerie Oberchain, Martin Morgan, Michael Lawrence. VariantAnnotation: Annotation of Genetic Variants. doi:10.18129/B9.bioc.VariantAnnotation, R package version 1.58.0, https://bioconductor.org/packages/VariantAnnotation.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantAnnotation")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.58.0 |
| License | Artistic-2.0 |
| System Requirements | GNU make |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 years) |
| Downloads rank | 80 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation |
| Package Short Url | https://bioconductor.org/packages/VariantAnnotation/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("VariantAnnotation")| Introduction to VariantAnnotation | HTML | R Script |
| Using filterVcf() to Select Variants from VCF Files | HTML | R Script |
| ensemblVEP: using the REST API with Bioconductor | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | VariantAnnotation_1.58.0.tar.gz |
| Windows binary (x86_64) | VariantAnnotation_1.58.0.zip |
| macOS binary (arm64) | VariantAnnotation_1.58.0.tgz |
| macOS binary (x86_64) | VariantAnnotation_1.58.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VariantAnnotation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VariantAnnotation |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1)
Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4), curl
LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0)
Suggests: GenomeInfoDb, 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, knitr, magick, jsonlite, httr, rjsoncons
Reverse dependencies
Depends On Me (23): alabaster.vcf, annotation, CNVrd2, deepSNV, demuxSNP, HelloRanges, myvariant, PlasmaMutationDetector, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me (57): AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CCAFE, ClonalSim, CNVfilteR, CopyNumberPlots, COSMIC.67, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, fcScan, fRagmentomics, G4SNVHunter, GA4GHclient, GenomicFiles, GenVisR, ggbio, gmapR, gpcp, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, MutSeqR, parati, ProteoDisco, RAIDS, scoreInvHap, SEMPLR, signeR, SigsPack, SNPhood, svaRetro, tadar, tLOH, transmogR, TVTB, Uniquorn, UPDhmm, VCFArray, YAPSA, ZygosityPredictor
Suggests Me (31): alabaster.files, AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CrispRVariants, epialleleR, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, igvShiny, ldblock, ldsep, MoBPS, omicsPrint, podkat, polyRAD, Rsamtools, RVS, SeqArray, shiny.gosling, SNPassoc, splatter, supersigs, systemPipeR, trackViewer, trio, updog, vtpnet