VariantAnnotation: Annotation of Genetic Variants

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

AuthorValerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]
Date of publicationNone
MaintainerValerie Obenchain <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.20.3

View on Bioconductor

Functions

AllVariants Man page
AllVariants-class Man page
alt Man page
alt<- Man page
alt<-,CollapsedVCF,CharacterList-method Man page
alt<-,CollapsedVCF,DNAStringSetList-method Man page
altDepth Man page
altDepth<- Man page
altDepth<-,VRanges-method Man page
altDepth,VRanges-method Man page
alt<-,ExpandedVCF,character-method Man page
alt<-,ExpandedVCF,DNAStringSet-method Man page
altFraction Man page
altFraction,VRanges-method Man page
alt,VCF-method Man page
alt<-,VRanges,ANY-method Man page
alt,VRanges-method Man page
asVCF Man page
asVCF,VRanges-method Man page
called Man page
called,VRanges-method Man page
cbind,VCF-method Man page
characterOrRle-class Man page
characterRle-class Man page
class:CollapsedVCF Man page
class:CompressedVRangesList Man page
class:ExpandedVCF Man page
class:PolyPhenDb Man page
class:PROVEANDb Man page
class:SIFTDb Man page
class:SimpleVRangesList Man page
class:VCF Man page
class:VRanges Man page
class:VRangesList Man page
CodingVariants Man page
CodingVariants-class Man page
coerce,GRanges,VRanges-method Man page
coerce,VCF,VRanges-method Man page
coerce,VRanges,VCF-method Man page
CollapsedVCF Man page
CollapsedVCF-class Man page
columns,PolyPhenDb-method Man page
columns,PROVEANDb-method Man page
columns,SIFTDb-method Man page
complexRle-class Man page
CompressedVRangesList-class Man page
contig Man page
contig,VCFHeader-method Man page
dbSNPFilter Man page
dimnames<-,VCF,list-method Man page
downstream Man page
downstream<- Man page
downstream<-,AllVariants-method Man page
downstream,AllVariants-method Man page
downstream<-,IntergenicVariants-method Man page
downstream,IntergenicVariants-method Man page
downstream<-,PromoterVariants-method Man page
downstream,PromoterVariants-method Man page
duplicateRSID Man page
expand,CollapsedVCF-method Man page
ExpandedVCF Man page
ExpandedVCF-class Man page
expand,ExpandedVCF-method Man page
factorOrRle-class Man page
factorRle-class Man page
filt Man page
filt<- Man page
filterVcf Man page
filterVcf,character-method Man page
filterVcf,TabixFile-method Man page
filt<-,VCF,character-method Man page
filt,VCF-method Man page
FiveUTRVariants Man page
FiveUTRVariants-class Man page
fixed Man page
fixed<- Man page
fixed<-,VCF,DataFrame-method Man page
fixed<-,VCFHeader,DataFrameList-method Man page
fixed,VCFHeader-method Man page
fixed,VCF-method Man page
geno Man page
geno<- Man page
genome,VCF-method Man page
genotypeCodesToNucleotides Man page
genotypeToSnpMatrix Man page
genotypeToSnpMatrix,array-method Man page
genotypeToSnpMatrix,CollapsedVCF-method Man page
geno,VCF,ANY-method Man page
geno<-,VCF,character,matrix-method Man page
geno,VCF,character-method Man page
geno,VCFHeader,ANY-method Man page
geno,VCFHeader-method Man page
geno<-,VCFHeader,missing,DataFrame-method Man page
geno,VCF-method Man page
geno<-,VCF,missing,matrix-method Man page
geno<-,VCF,missing,SimpleList-method Man page
geno<-,VCF,numeric,matrix-method Man page
geno,VCF,numeric-method Man page
getTranscriptSeqs Man page
getTranscriptSeqs,GRanges,FaFile-method Man page
getTranscriptSeqs,GRangesList,ANY-method Man page
getTranscriptSeqs,GRangesList,BSgenome-method Man page
getTranscriptSeqs,GRangesList,FaFile-method Man page
GLtoGP Man page
hardFilters Man page
hardFilters<- Man page
hardFilters<-,VRanges-method Man page
hardFilters,VRanges-method Man page
header Man page
header<- Man page
header,VCFHeader-method Man page
header,VCF-method Man page
header<-,VCF,VCFHeader-method Man page
import,VcfFile,ANY,ANY-method Man page
info Man page
info<- Man page
info<-,VCF,DataFrame-method Man page
info<-,VCFHeader,DataFrame-method Man page
info,VCFHeader-method Man page
info,VCF-method Man page
integerOrRle-class Man page
integerRle-class Man page
intergenic Man page
intergenic<- Man page
intergenic<-,AllVariants-method Man page
intergenic,AllVariants-method Man page
IntergenicVariants Man page
IntergenicVariants-class Man page
IntronVariants Man page
IntronVariants-class Man page
isDeletion Man page
isDeletion,CollapsedVCF-method Man page
isDeletion,ExpandedVCF-method Man page
isDeletion,VRanges-method Man page
isDelins Man page
isDelins,CollapsedVCF-method Man page
isDelins,ExpandedVCF-method Man page
isDelins,VRanges-method Man page
isIndel Man page
isIndel,CollapsedVCF-method Man page
isIndel,ExpandedVCF-method Man page
isIndel,VRanges-method Man page
isInsertion Man page
isInsertion,CollapsedVCF-method Man page
isInsertion,ExpandedVCF-method Man page
isInsertion,VRanges-method Man page
isSNV Man page
isSNV,CollapsedVCF-method Man page
isSNV,ExpandedVCF-method Man page
isSNV,VRanges-method Man page
isSubstitution Man page
isSubstitution,CollapsedVCF-method Man page
isSubstitution,ExpandedVCF-method Man page
isSubstitution,VRanges-method Man page
isTransition Man page
isTransition,CollapsedVCF-method Man page
isTransition,ExpandedVCF-method Man page
isTransition,VRanges-method Man page
keys,PolyPhenDb-method Man page
keys,PROVEANDb-method Man page
keys,SIFTDb-method Man page
keytypes,PROVEANDb-method Man page
locateVariants Man page
locateVariants,GRanges,GRangesList,AllVariants-method Man page
locateVariants,GRanges,GRangesList,CodingVariants-method Man page
locateVariants,GRanges,GRangesList,FiveUTRVariants-method Man page
locateVariants,GRanges,GRangesList,IntergenicVariants-method Man page
locateVariants,GRanges,GRangesList,IntronVariants-method Man page
locateVariants,GRanges,GRangesList,PromoterVariants-method Man page
locateVariants,GRanges,GRangesList,SpliceSiteVariants-method Man page
locateVariants,GRanges,GRangesList,ThreeUTRVariants-method Man page
locateVariants,GRanges,GRangesList,VariantType-method Man page
locateVariants,GRanges,TxDb,AllVariants-method Man page
locateVariants,GRanges,TxDb,CodingVariants-method Man page
locateVariants,GRanges,TxDb,FiveUTRVariants-method Man page
locateVariants,GRanges,TxDb,IntergenicVariants-method Man page
locateVariants,GRanges,TxDb,IntronVariants-method Man page
locateVariants,GRanges,TxDb,PromoterVariants-method Man page
locateVariants,GRanges,TxDb,SpliceSiteVariants-method Man page
locateVariants,GRanges,TxDb,ThreeUTRVariants-method Man page
locateVariants,GRanges,TxDb,VariantType-method Man page
locateVariants,Ranges,GRangesList,VariantType-method Man page
locateVariants,Ranges,TxDb,VariantType-method Man page
locateVariants,VCF,GRangesList,VariantType-method Man page
locateVariants,VCF,TxDb,VariantType-method Man page
logicalRle-class Man page
makeVRangesFromGRanges Man page
match,VRanges,VRanges-method Man page
MatrixToSnpMatrix Man page
mcols<-,VCF,DataFrame-method Man page
meta Man page
meta<- Man page
metadata,PolyPhenDb-method Man page
metadata,SIFTDb-method Man page
meta<-,VCFHeader,DataFrameList-method Man page
meta<-,VCFHeader,DataFrame-method Man page
meta,VCFHeader-method Man page
numericRle-class Man page
PLtoGP Man page
PolyPhen Man page
PolyPhenDb Man page
PolyPhenDb-class Man page
PolyPhenDbColumns Man page
predictCoding Man page
predictCoding,CollapsedVCF,TxDb,ANY,missing-method Man page
predictCoding,ExpandedVCF,TxDb,ANY,missing-method Man page
predictCoding,GRanges,TxDb,ANY,DNAStringSet-method Man page
predictCoding,Ranges,TxDb,ANY,DNAStringSet-method Man page
predictCoding,VRanges,TxDb,ANY,missing-method Man page
probabilityToSnpMatrix Man page
promoter Man page
promoter<- Man page
promoter<-,AllVariants-method Man page
promoter,AllVariants-method Man page
PromoterVariants Man page
PromoterVariants-class Man page
PROVEAN Man page
PROVEANDb Man page
PROVEANDb-class Man page
qual Man page
qual<- Man page
qual,VCF-method Man page
qual<-,VCF,numeric-method Man page
rawRle-class Man page
rbind,VCF-method Man page
readGeno Man page
readGT Man page
readInfo Man page
readVcf Man page
readVcfAsVRanges Man page
readVcf,character,ANY-method Man page
readVcf,character,missing-method Man page
readVcf,character,missing-method Man page
readVcfLongForm Man page
readVcfLongForm,character,character,missing-method Man page
readVcfLongForm,character,character,ScanVcfParam-method Man page
readVcfLongForm,character,missing,missing-method Man page
readVcfLongForm,TabixFile,character,GRanges-method Man page
readVcfLongForm,TabixFile,character,missing-method Man page
readVcfLongForm,TabixFile,character,RangesList-method Man page
readVcfLongForm,TabixFile,character,ScanVcfParam-method Man page
readVcf,TabixFile,GRangesList-method Man page
readVcf,TabixFile,GRanges-method Man page
readVcf,TabixFile,missing-method Man page
readVcf,TabixFile,RangesList-method Man page
readVcf,TabixFile,ScanVcfParam-method Man page
ref Man page
ref<- Man page
refDepth Man page
refDepth<- Man page
refDepth<-,VRanges-method Man page
refDepth,VRanges-method Man page
reference Man page
reference,VCFHeader-method Man page
refLocsToLocalLocs Man page
refLocsToLocalLocs,GRanges,missing,GRangesList-method Man page
refLocsToLocalLocs,GRanges,TxDb,missing-method Man page
ref<-,VCF,DNAStringSet-method Man page
ref,VCF-method Man page
ref<-,VRanges,ANY-method Man page
ref,VRanges-method Man page
regionFilter Man page
resetFilter Man page
restrictToSNV Man page
rowRanges<-,VCF-method Man page
rowRanges,VCF-method Man page
sampleNames<-,VRanges,ANY-method Man page
sampleNames,VRanges-method Man page
samples Man page
samples,VCFHeader-method Man page
scanVcf Man page
scanVcf,character,missing-method Man page
scanVcf,character,ScanVcfParam-method Man page
scanVcf,connection,missing-method Man page
scanVcfHeader Man page
scanVcfHeader,character-method Man page
scanVcfHeader,TabixFile-method Man page
ScanVcfParam Man page
ScanVcfParam,ANY-method Man page
ScanVcfParam-class Man page
ScanVcfParam,missing-method Man page
scanVcf,TabixFile,GRanges-method Man page
scanVcf,TabixFile,missing-method Man page
scanVcf,TabixFile,RangesList-method Man page
scanVcf,TabixFile,ScanVcfParam-method Man page
select,PolyPhenDb-method Man page
select,PROVEANDb-method Man page
select,SIFTDb-method Man page
seqinfo,VCFHeader-method Man page
seqlevels,VCF-method Man page
show,AllVariants-method Man page
show,CollapsedVCF-method Man page
show,ExpandedVCF-method Man page
show,PromoterVariants-method Man page
show,VariantType-method Man page
show,VCFHeader-method Man page
show,VCF-method Man page
SIFT Man page
SIFTDb Man page
SIFTDb-class Man page
SIFTDbColumns Man page
SimpleVRangesList-class Man page
SnpMatrixToVCF Man page
snpSummary Man page
snpSummary,CollapsedVCF-method Man page
softFilter Man page
softFilterMatrix Man page
softFilterMatrix<- Man page
softFilterMatrix<-,VRanges-method Man page
softFilterMatrix,VRanges-method Man page
SpliceSiteVariants Man page
SpliceSiteVariants-class Man page
stackSamples Man page
stackSamples,VRangesList-method Man page
strand<-,VCF,ANY-method Man page
strand,VCF-method Man page
summarizeVariants Man page
summarizeVariants,GRangesList,VCF,function-method Man page
summarizeVariants,GRangesList,VCF,VariantType-method Man page
summarizeVariants,TxDb,VCF,CodingVariants-method Man page
summarizeVariants,TxDb,VCF,FiveUTRVariants-method Man page
summarizeVariants,TxDb,VCF,IntronVariants-method Man page
summarizeVariants,TxDb,VCF,PromoterVariants-method Man page
summarizeVariants,TxDb,VCF,SpliceSiteVariants-method Man page
summarizeVariants,TxDb,VCF,ThreeUTRVariants-method Man page
tabulate Man page
tabulate,VRanges-method Man page
ThreeUTRVariants Man page
ThreeUTRVariants-class Man page
totalDepth Man page
totalDepth<- Man page
totalDepth<-,VRanges-method Man page
totalDepth,VRanges-method Man page
upstream Man page
upstream<- Man page
upstream<-,AllVariants-method Man page
upstream,AllVariants-method Man page
upstream<-,IntergenicVariants-method Man page
upstream,IntergenicVariants-method Man page
upstream<-,PromoterVariants-method Man page
upstream,PromoterVariants-method Man page
VariantAnnotation-defunct Man page
VariantType-class Man page
VCF Man page
[,VCF,ANY,ANY-method Man page
[<-,VCF,ANY,ANY,VCF-method Man page
VCF-class Man page
VcfFile Man page
VcfFile-class Man page
VcfFileList Man page
VcfFileList-class Man page
vcfFixed Man page
vcfFixed<- Man page
vcfGeno Man page
vcfGeno<- Man page
VCFHeader Man page
VCFHeader-class Man page
vcfInfo Man page
vcfInfo<- Man page
[,VCF-method Man page
vcfSamples Man page
vcfSamples<- Man page
vcfTrimEmpty Man page
vcfTrimEmpty<- Man page
vcfWhich Man page
vcfWhich<- Man page
VRanges Man page
VRanges Man page
VRanges-class Man page
VRangesList Man page
VRangesList-class Man page
VRangesScanVcfParam Man page
writeVcf Man page
writeVcf,VCF,character-method Man page
writeVcf,VCF,connection-method Man page
writeVcf,VRanges,ANY-method Man page

Files

VariantAnnotation/DESCRIPTION
VariantAnnotation/NAMESPACE
VariantAnnotation/NEWS
VariantAnnotation/R
VariantAnnotation/R/AllClasses.R VariantAnnotation/R/AllGenerics.R VariantAnnotation/R/AllUtilities.R VariantAnnotation/R/makeVRangesFromGRanges.R VariantAnnotation/R/methods-CollapsedVCF-class.R VariantAnnotation/R/methods-ExpandedVCF-class.R VariantAnnotation/R/methods-PROVEANDb.class.R VariantAnnotation/R/methods-PolyPhenDb-class.R VariantAnnotation/R/methods-SIFTDb-class.R VariantAnnotation/R/methods-ScanVcfParam-class.R VariantAnnotation/R/methods-VCF-class.R VariantAnnotation/R/methods-VCFHeader-class.R VariantAnnotation/R/methods-VRanges-class.R VariantAnnotation/R/methods-VRangesList-class.R VariantAnnotation/R/methods-VariantType-class.R VariantAnnotation/R/methods-VcfFile.R VariantAnnotation/R/methods-expand.R VariantAnnotation/R/methods-filterVcf.R VariantAnnotation/R/methods-genotypeToSnpMatrix.R VariantAnnotation/R/methods-import.R VariantAnnotation/R/methods-locateVariants.R VariantAnnotation/R/methods-predictCoding.R VariantAnnotation/R/methods-readVcf.R VariantAnnotation/R/methods-scanVcf.R VariantAnnotation/R/methods-scanVcfHeader.R VariantAnnotation/R/methods-snpSummary.R VariantAnnotation/R/methods-summarizeVariants.R VariantAnnotation/R/methods-writeVcf.R VariantAnnotation/R/test_VariantAnnotation_package.R
VariantAnnotation/build
VariantAnnotation/build/vignette.rds
VariantAnnotation/inst
VariantAnnotation/inst/CITATION
VariantAnnotation/inst/doc
VariantAnnotation/inst/doc/VariantAnnotation.R
VariantAnnotation/inst/doc/VariantAnnotation.Rnw
VariantAnnotation/inst/doc/VariantAnnotation.pdf
VariantAnnotation/inst/doc/filterVcf.R
VariantAnnotation/inst/doc/filterVcf.Rnw
VariantAnnotation/inst/doc/filterVcf.pdf
VariantAnnotation/inst/extdata
VariantAnnotation/inst/extdata/chr22.vcf.gz
VariantAnnotation/inst/extdata/chr22.vcf.gz.tbi
VariantAnnotation/inst/extdata/chr7-sub.vcf.gz
VariantAnnotation/inst/extdata/chr7-sub.vcf.gz.tbi
VariantAnnotation/inst/extdata/ex2.vcf
VariantAnnotation/inst/extdata/gl_chr1.vcf
VariantAnnotation/inst/extdata/h1187-10k.vcf.gz
VariantAnnotation/inst/extdata/h1187-10k.vcf.gz.tbi
VariantAnnotation/inst/extdata/hapmap_exome_chr22.vcf.gz
VariantAnnotation/inst/extdata/hapmap_exome_chr22.vcf.gz.tbi
VariantAnnotation/inst/extdata/structural.vcf
VariantAnnotation/inst/scripts
VariantAnnotation/inst/scripts/test_Rplinkseq.R
VariantAnnotation/inst/unitTests
VariantAnnotation/inst/unitTests/cases
VariantAnnotation/inst/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf
VariantAnnotation/inst/unitTests/cases/VarScan_header.vcf
VariantAnnotation/inst/unitTests/cases/banded_gvcf.vcf
VariantAnnotation/inst/unitTests/cases/expand.vcf
VariantAnnotation/inst/unitTests/cases/fewer-FORMAT-than-GENO.vcf
VariantAnnotation/inst/unitTests/cases/missing-FORMAT-metadata-elt.vcf
VariantAnnotation/inst/unitTests/cases/mixedStructural.vcf
VariantAnnotation/inst/unitTests/cases/multiple_INFO_fields.vcf
VariantAnnotation/inst/unitTests/cases/negative_FORMAT_Number.vcf
VariantAnnotation/inst/unitTests/cases/no_FORMAT_column.vcf
VariantAnnotation/inst/unitTests/cases/no_GENO_row.vcf
VariantAnnotation/inst/unitTests/cases/no_INFO_header.vcf
VariantAnnotation/inst/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf
VariantAnnotation/inst/unitTests/test_SIFTandPolyPhen.R
VariantAnnotation/inst/unitTests/test_ScanVcfParam-class.R
VariantAnnotation/inst/unitTests/test_VCF-class.R
VariantAnnotation/inst/unitTests/test_VRanges-class.R
VariantAnnotation/inst/unitTests/test_expand-methods.R
VariantAnnotation/inst/unitTests/test_filterVcf.R
VariantAnnotation/inst/unitTests/test_genotypeToSnpMatrix.R
VariantAnnotation/inst/unitTests/test_isSNV.R
VariantAnnotation/inst/unitTests/test_locateVariants-methods.R
VariantAnnotation/inst/unitTests/test_predictCoding-methods.R
VariantAnnotation/inst/unitTests/test_readVcf-methods.R
VariantAnnotation/inst/unitTests/test_scanVcf.R
VariantAnnotation/inst/unitTests/test_snpSummary.R
VariantAnnotation/inst/unitTests/test_summarizeVariants-methods.R
VariantAnnotation/inst/unitTests/test_writeVcf-methods.R
VariantAnnotation/man
VariantAnnotation/man/GLtoGP.Rd VariantAnnotation/man/PROVEANDb-class.Rd VariantAnnotation/man/PolyPhenDb-class.Rd VariantAnnotation/man/PolyPhenDbColumns.Rd VariantAnnotation/man/SIFTDb-class.Rd VariantAnnotation/man/SIFTDbColumns.Rd VariantAnnotation/man/ScanVcfParam-class.Rd VariantAnnotation/man/VCF-class.Rd VariantAnnotation/man/VCFHeader-class.Rd VariantAnnotation/man/VRanges-class.Rd VariantAnnotation/man/VRangesList-class.Rd VariantAnnotation/man/VariantType-class.Rd VariantAnnotation/man/VcfFile-class.Rd VariantAnnotation/man/defunct.Rd VariantAnnotation/man/filterVcf-methods.Rd VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd VariantAnnotation/man/getTranscriptSeqs-methods.Rd VariantAnnotation/man/isSNV-methods.Rd VariantAnnotation/man/locateVariants-methods.Rd VariantAnnotation/man/predictCoding-methods.Rd VariantAnnotation/man/probabilityToSnpMatrix.Rd VariantAnnotation/man/readVcf-methods.Rd VariantAnnotation/man/scanVcf-methods.Rd VariantAnnotation/man/snpSummary.Rd VariantAnnotation/man/summarizeVariants-methods.Rd VariantAnnotation/man/writeVcf-methods.Rd
VariantAnnotation/src
VariantAnnotation/src/Biostrings_stubs.c
VariantAnnotation/src/IRanges_stubs.c
VariantAnnotation/src/Makevars
VariantAnnotation/src/Makevars.win
VariantAnnotation/src/R_init_VariantAnnotation.c
VariantAnnotation/src/XVector_stubs.c
VariantAnnotation/src/dna_hash.c
VariantAnnotation/src/dna_hash.h
VariantAnnotation/src/rle.c
VariantAnnotation/src/rle.h
VariantAnnotation/src/strhash.c
VariantAnnotation/src/strhash.h
VariantAnnotation/src/utilities.c
VariantAnnotation/src/utilities.h
VariantAnnotation/src/vcffile.c
VariantAnnotation/src/vcffile.h
VariantAnnotation/src/vcftype.c
VariantAnnotation/src/vcftype.h
VariantAnnotation/src/writevcf.c
VariantAnnotation/src/writevcf.h
VariantAnnotation/tests
VariantAnnotation/tests/VariantAnnotation_unit_tests.R
VariantAnnotation/vignettes
VariantAnnotation/vignettes/VariantAnnotation.Rnw
VariantAnnotation/vignettes/filterVcf.Rnw
VariantAnnotation/vignettes/filterVcf.bib

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