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VariantAnnotation

Annotation of Genetic Variants


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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.

Documentation

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

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

Details

biocViews Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.48.1
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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)
System Requirements GNU make
URL
See More
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, knitr
Linking To S4Vectors, IRanges, XVector, Biostrings, Rhtslib(>= 1.99.3)
Enhances
Depends On Me alabaster.vcf, annotation, CNVrd2, deepSNV, demuxSNP, ensemblVEP, 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, RAIDS, scoreInvHap, SigsPack, SNPhood, svaRetro, tadar, TitanCNA, tLOH, TVTB, Uniquorn, VCFArray, YAPSA, ZygosityPredictor
Suggests Me alabaster.files, 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 Build Report

Package Archives

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

Source Package VariantAnnotation_1.48.1.tar.gz
Windows Binary VariantAnnotation_1.48.1.zip
macOS Binary (x86_64) VariantAnnotation_1.48.1.tgz
macOS Binary (arm64) VariantAnnotation_1.48.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/VariantAnnotation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantAnnotation
Bioc Package Browser https://code.bioconductor.org/browse/VariantAnnotation/
Package Short Url https://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive