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## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

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VariantAnnotation

DOI: 10.18129/B9.bioc.VariantAnnotation

Annotation of Genetic Variants

Bioconductor version: Release (3.5)

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")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

Documentation

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

browseVignettes("VariantAnnotation")

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

Details

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.22.3
In Bioconductor since	BioC 2.9 (R-2.14) (6 years)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.15.3), GenomeInfoDb(>= 1.11.4), GenomicRanges(>= 1.27.6), SummarizedExperiment(>= 1.5.3), Rsamtools(>= 1.23.10)
Imports	utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.13.13), IRanges(>= 2.3.25), XVector(>= 0.5.6), Biostrings(>= 2.33.5), AnnotationDbi(>= 1.27.9), BSgenome(>= 1.37.6), rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.27.4)
LinkingTo	S4Vectors, IRanges, XVector, Biostrings, Rsamtools
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
SystemRequirements
Enhances
URL
Depends On Me	ampliQueso, cgdv17, CNVrd2, deepSNV, DOQTL, ensemblVEP, genotypeeval, GoogleGenomics, HelloRanges, HTSeqGenie, myvariant, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, Rariant, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, VariantFiltering, VariantTools, VariantToolsData
Imports Me	AllelicImbalance, BadRegionFinder, BBCAnalyzer, biovizBase, COSMIC.67, customProDB, FunciSNP, GA4GHclient, genbankr, GenomicFiles, ggbio, GGtools, gmapR, gQTLstats, gwascat, ldblock, MADSEQ, maftools, methyAnalysis, motifbreakR, MutationalPatterns, PGA, SeqArray, SeqVarTools, signeR, SNPhood, systemPipeR, TVTB, YAPSA
Suggests Me	AnnotationHub, AshkenazimSonChr21, cellbaseR, CrispRVariants, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GMRP, GWASTools, podkat, trackViewer, trio, vtpnet
Build Report

Package Archives

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

Source Package	VariantAnnotation_1.22.3.tar.gz
Windows Binary	VariantAnnotation_1.22.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	VariantAnnotation_1.22.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantAnnotation
Package Short Url	http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report	Download Stats

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