VariantAnnotation

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.9

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

Author: Valerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]

Maintainer: Valerie Obenchain <maintainer at bioconductor.org>

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

To install this package, start R (version "3.6") 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.

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

browseVignettes("VariantAnnotation")

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

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.30.1
In Bioconductor since	BioC 2.9 (R-2.14) (12.5 years)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.15.3), GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.31.8), SummarizedExperiment(>= 1.9.9), Rsamtools(>= 1.99.0)
Imports	utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.17.24), IRanges(>= 2.13.13), XVector(>= 0.19.7), Biostrings(>= 2.47.6), AnnotationDbi(>= 1.27.9), rtracklayer(>= 1.39.7), BSgenome(>= 1.47.3), GenomicFeatures(>= 1.31.3)
System Requirements
URL

Suggests	RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
Linking To	S4Vectors, IRanges, XVector, Biostrings, Rhtslib
Enhances
Depends On Me	annotation, cgdv17, CNVrd2, deepSNV, DOQTL, ensemblVEP, genotypeeval, HelloRanges, HTSeqGenie, igvR, MTseeker, myvariant, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, Rariant, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, signeR, SomaticSignatures, StructuralVariantAnnotation, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me	AllelicImbalance, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, CopyNumberPlots, COSMIC.67, customProDB, decompTumor2Sig, DominoEffect, FunciSNP, GA4GHclient, genbankr, GenomicFiles, GenVisR, ggbio, GGtools, gmapR, gQTLstats, gwasurvivr, icetea, ldblock, MADSEQ, methyAnalysis, motifbreakR, MTseekerData, MutationalPatterns, PGA, scoreInvHap, SNPhood, systemPipeR, TitanCNA, TVTB, Uniquorn, VCFArray, YAPSA, yriMulti
Suggests Me	AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CrispRVariants, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, gwascat, GWASTools, omicsPrint, podkat, RVS, SeqArray, trackViewer, trio, vtpnet
Links To Me
Build Report	Build Report

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

Source Package	VariantAnnotation_1.30.1.tar.gz
Windows Binary	VariantAnnotation_1.30.1.zip
Mac OS X 10.11 (El Capitan)	VariantAnnotation_1.30.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantAnnotation
Source Repository (Developer Access)	git clone [email protected]: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 3.9	Source Archive