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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>

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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


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
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
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