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Annotation of Genetic Variants

Bioconductor version: 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>

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


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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
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
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Package Source VariantAnnotation_1.14.13.tar.gz
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