This package is for version 3.12 of Bioconductor;
for the stable, up-to-date release version, see
VariantAnnotation.
Annotation of Genetic Variants
Bioconductor version: 3.12
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Author: Bioconductor Package Maintainer [aut, cre], Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R, enter citation("VariantAnnotation")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantAnnotation")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("VariantAnnotation")
2. Using filterVcf to Select Variants from VCF Files
PDF
R Script
Details
Version
1.36.0
In Bioconductor since
BioC 2.9 (R-2.14) (12.5 years)
License
Artistic-2.0
Imports
utils, DBI,
zlibbioc,
Biobase,
S4Vectors(>= 0.27.12),
IRanges(>= 2.23.9),
XVector(>= 0.29.2),
Biostrings(>= 2.57.2),
AnnotationDbi(>= 1.27.9),
rtracklayer(>= 1.39.7),
BSgenome(>= 1.47.3),
GenomicFeatures(>= 1.31.3)
System Requirements
GNU make
See More
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
Enhances
Depends On Me
annotation,
cgdv17,
CNVrd2,
deepSNV,
ensemblVEP,
genotypeeval,
HelloRanges,
HTSeqGenie,
myvariant,
PolyPhen.Hsapiens.dbSNP131,
PureCN,
R453Plus1Toolbox,
RareVariantVis,
Rariant,
seqCAT,
sequencing,
SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137,
signeR,
SomaticSignatures,
StructuralVariantAnnotation,
VariantFiltering,
variants,
VariantTools,
VariantToolsData
Imports Me
AllelicImbalance,
APAlyzer,
appreci8R,
BadRegionFinder,
BBCAnalyzer,
biovizBase,
biscuiteer,
CNVfilteR,
CopyNumberPlots,
COSMIC.67,
customProDB,
DAMEfinder,
decompTumor2Sig,
DominoEffect,
fcScan,
FunciSNP,
GA4GHclient,
genbankr,
GenomicFiles,
GenVisR,
ggbio,
GGtools,
gmapR,
gQTLstats,
gwascat,
gwasurvivr,
icetea,
igvR,
karyoploteR,
ldblock,
MADSEQ,
methyAnalysis,
MMAPPR2,
motifbreakR,
musicatk,
MutationalPatterns,
PGA,
scoreInvHap,
SigsPack,
SNPhood,
systemPipeR,
TitanCNA,
TVTB,
Uniquorn,
VCFArray,
XCIR,
YAPSA,
yriMulti
Suggests Me
AnnotationHub,
AshkenazimSonChr21,
BiocParallel,
cellbaseR,
CrispRVariants,
GenomicRanges,
GenomicScores,
GeuvadisTranscriptExpr,
GWASTools,
omicsPrint,
podkat,
RVS,
SeqArray,
splatter,
trackViewer,
trio,
vtpnet
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/VariantAnnotation
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/VariantAnnotation