To install this package, start R and enter:

source("http://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: 2.14

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

Author: Valerie Obenchain, Martin Morgan, Michael Lawrence with contributions from Stephanie Gogarten.

Maintainer: Valerie Obenchain <vobencha at fhcrc.org>

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

To install this package, start R and enter:

source("http://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

biocViews	Annotation, DataImport, Genetics, Homo_sapiens, SNP, Sequencing, Software
Version	1.10.5
In Bioconductor since	BioC 2.9 (R-2.14)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.7.7), GenomicRanges(>= 1.13.51), Rsamtools(>= 1.15.5)
Imports	IRanges(>= 1.21.43), XVector, Biostrings(>= 2.31.19), Biobase, AnnotationDbi(>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures(>= 1.15.15), DBI, utils, rtracklayer
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
System Requirements
URL
Depends On Me	ampliQueso, cgdv17, CNVrd2, deepSNV, ensemblVEP, HTSeqGenie, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, VariantTools
Imports Me	biovizBase, COSMIC.67, customProDB, FunciSNP, ggbio, GGtools, gmapR, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, R453Plus1Toolbox, Rariant, SeqArray, SomaticSignatures, VariantFiltering
Suggests Me	GenomicRanges, GWASTools, trio, vtpnet

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