To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

In most cases, you don't need to download the package archive at all.

VariantAnnotation

Annotation of Genetic Variants

Bioconductor version: Release (3.1)

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 <vobencha at fhcrc.org>

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

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")

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

browseVignettes("VariantAnnotation")

PDF	R Script	filterVcf Overview
PDF	R Script	Introduction to VariantAnnotation
PDF		Reference Manual
Text		NEWS
Video		Reading VCF data

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.14.13
In Bioconductor since	BioC 2.9 (R-2.14) (4 years)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.7.7), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.19.47), Rsamtools(>= 1.19.52)
Imports	utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.5.14), IRanges(>= 2.1.27), XVector(>= 0.5.6), Biostrings(>= 2.33.5), AnnotationDbi(>= 1.27.9), BSgenome, rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.19.17)
LinkingTo	S4Vectors, IRanges, XVector, Biostrings, Rsamtools
Suggests	RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me	AllelicImbalance, ampliQueso, cgdv17, CNVrd2, deepSNV, ensemblVEP, GoogleGenomics, HTSeqGenie, PolyPhen.Hsapiens.dbSNP131, Rariant, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, VariantFiltering, VariantTools
Imports Me	AllelicImbalance, biovizBase, COSMIC.67, customProDB, FunciSNP, ggbio, GGtools, gmapR, gQTLstats, gwascat, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, methyAnalysis, R453Plus1Toolbox, SeqArray, SeqVarTools, systemPipeR
Suggests Me	AnnotationHub, GenomicRanges, GWASTools, podkat, trio, vtpnet
Build Report

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

Package Source	VariantAnnotation_1.14.13.tar.gz
Windows Binary	VariantAnnotation_1.14.13.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	VariantAnnotation_1.14.13.tgz
Mac OS X 10.9 (Mavericks)	VariantAnnotation_1.14.13.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-3.1
Package Short Url	http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report	Download Stats

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