To install this package, start R and enter:

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

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

VariantAnnotation

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.2

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

Details

biocViews	Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.16.4
In Bioconductor since	BioC 2.9 (R-2.14) (4.5 years)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.15.3), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.19.47), SummarizedExperiment(>= 0.3.1), Rsamtools(>= 1.19.52)
Imports	utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.7.11), 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(>= 1.19.17)
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, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me	ampliQueso, cgdv17, CNVrd2, deepSNV, DOQTL, ensemblVEP, genotypeeval, GoogleGenomics, HTSeqGenie, myvariant, PolyPhen.Hsapiens.dbSNP131, R453Plus1Toolbox, RareVariantVis, Rariant, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, VariantFiltering, VariantTools
Imports Me	AllelicImbalance, BBCAnalyzer, 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.ALL.wgs.phase3.release.v5b.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, methyAnalysis, motifbreakR, PGA, SeqArray, SeqVarTools, SNPhood, systemPipeR
Suggests Me	AnnotationHub, AshkenazimSonChr21, GenomicRanges, GWASTools, podkat, trio, vtpnet
Build Report

Package Archives

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

Package Source	VariantAnnotation_1.16.4.tar.gz
Windows Binary	VariantAnnotation_1.16.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	VariantAnnotation_1.16.3.tgz
Mac OS X 10.9 (Mavericks)	VariantAnnotation_1.16.4.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-3.2
Package Short Url	http://bioconductor.org/packages/VariantAnnotation/
Package Downloads Report	Download Stats

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