VariantAnnotation

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.14

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 bioconductor.org>

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

Installation

To install this package, start R (version "4.1") 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	PDF	R Script
2. Using filterVcf to Select Variants from VCF Files	PDF	R Script
Reference Manual	PDF
NEWS	Text
Reading VCF data	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.40.0
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

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, 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, CNVfilteR, CopyNumberPlots, COSMIC.67, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, epialleleR, fcScan, GA4GHclient, genbankr, GenomicFiles, GenVisR, ggbio, gmapR, gwascat, gwasurvivr, icetea, igvR, karyoploteR, ldblock, MADSEQ, MMAPPR2, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, ProteoDisco, scoreInvHap, SigsPack, SNPhood, svaRetro, TitanCNA, tLOH, TVTB, Uniquorn, VCFArray, XCIR, YAPSA
Suggests Me	AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CNVgears, CrispRVariants, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, 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_1.40.0.tar.gz
Windows Binary	VariantAnnotation_1.40.0.zip
macOS 10.13 (High Sierra)	VariantAnnotation_1.40.0.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 3.14	Source Archive