Package: VariantAnnotation 1.51.0

Bioconductor Package Maintainer

VariantAnnotation: Annotation of Genetic Variants

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

Authors:Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb], Bioconductor Package Maintainer [cre]

VariantAnnotation_1.51.0.tar.gz
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VariantAnnotation.pdf |VariantAnnotation.html✨
VariantAnnotation/json (API)
NEWS

# Install 'VariantAnnotation' in R:

install.packages('VariantAnnotation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library

On BioConductor:VariantAnnotation-1.51.0(bioc 3.20)VariantAnnotation-1.50.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

126 exports 7.20 score 69 dependencies 152 dependents 47 mentions

Last updated 2 months agofrom:6d549f2c16

Exports:AllVariants alt alt<-altDepth altDepth<-altFraction asVCF called cbind CodingVariants columns downstream downstream<-duplicateRSID expand filt filt<-filterVcf FiveUTRVariants fixed fixed<-geno geno<-genome genotypeCodesToNucleotides genotypeToSnpMatrix getSeq getTranscriptSeqs GLtoGP hardFilters hardFilters<-header header<-idType idType<-import indexVcf info info<-intergenic intergenic<-IntergenicVariants IntronVariants isDeletion isDelins isIndel isInsertion isSNV isSubstitution isTransition keys keytypes locateVariants makeVRangesFromGRanges mcols<-meta meta<-PLtoGP post_Hs_region predictCoding probabilityToSnpMatrix promoter promoter<-PromoterVariants qual qual<-rbind readGeno readGT readInfo readVcf readVcfAsVRanges ref ref<-refDepth refDepth<-reference resetFilter sampleNames sampleNames<-samples scanVcf scanVcfHeader ScanVcfParam select seqinfo seqlevels snpSummary softFilter softFilterMatrix softFilterMatrix<-SpliceSiteVariants stackSamples strand strand<-subset summarizeVariants tabulate ThreeUTRVariants totalDepth totalDepth<-updateObject upstream upstream<-VCF vcfFields VcfFile VcfFileList vcfFixed vcfFixed<-vcfGeno vcfGeno<-VCFHeader vcfInfo vcfInfo<-vcfSamples vcfSamples<-vcfTrimEmpty vcfTrimEmpty<-vcfWhich vcfWhich<-vep_by_region VRanges VRangesList VRangesScanVcfParam writeVcf

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML XVector yaml zlibbioc

Introduction to VariantAnnotation

Valerie Obenchain

Rendered fromVariantAnnotation.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-06-02
Started: 2023-06-02

Using filterVcf() to Select Variants from VCF Files

Paul Shannon

Rendered fromfilterVcf.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-06-02
Started: 2023-06-02

ensemblVEP: using the REST API with Bioconductor

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromensemblVEP.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-01-26
Started: 2024-01-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filter VCF files	filterVcf filterVcf,character-method filterVcf,TabixFile-method
Convert genotype calls from a VCF file to a SnpMatrix object	genotypeToSnpMatrix genotypeToSnpMatrix,array-method genotypeToSnpMatrix,CollapsedVCF-method
Get transcript sequences	getTranscriptSeqs getTranscriptSeqs,GRanges,FaFile-method getTranscriptSeqs,GRangesList,ANY-method getTranscriptSeqs,GRangesList,BSgenome-method getTranscriptSeqs,GRangesList,FaFile-method
Convert genotype likelihoods to genotype probabilities	GLtoGP PLtoGP
Create index files for VCF files	indexVcf indexVcf,character-method indexVcf,VcfFile-method indexVcf,VcfFileList-method
Identification of genomic variant types.	isDeletion isDeletion,CollapsedVCF-method isDeletion,ExpandedVCF-method isDeletion,VRanges-method isDelins isDelins,CollapsedVCF-method isDelins,ExpandedVCF-method isDelins,VRanges-method isIndel isIndel,CollapsedVCF-method isIndel,ExpandedVCF-method isIndel,VRanges-method isInsertion isInsertion,CollapsedVCF-method isInsertion,ExpandedVCF-method isInsertion,VRanges-method isSNV isSNV,CollapsedVCF-method isSNV,ExpandedVCF-method isSNV,VRanges-method isSubstitution isSubstitution,CollapsedVCF-method isSubstitution,ExpandedVCF-method isSubstitution,VRanges-method isTransition isTransition,CollapsedVCF-method isTransition,ExpandedVCF-method isTransition,VRanges-method
Locate variants	locateVariants locateVariants,GRanges,GRangesList,AllVariants-method locateVariants,GRanges,GRangesList,CodingVariants-method locateVariants,GRanges,GRangesList,FiveUTRVariants-method locateVariants,GRanges,GRangesList,IntergenicVariants-method locateVariants,GRanges,GRangesList,IntronVariants-method locateVariants,GRanges,GRangesList,PromoterVariants-method locateVariants,GRanges,GRangesList,SpliceSiteVariants-method locateVariants,GRanges,GRangesList,ThreeUTRVariants-method locateVariants,GRanges,GRangesList,VariantType-method locateVariants,GRanges,TxDb,AllVariants-method locateVariants,GRanges,TxDb,CodingVariants-method locateVariants,GRanges,TxDb,FiveUTRVariants-method locateVariants,GRanges,TxDb,IntergenicVariants-method locateVariants,GRanges,TxDb,IntronVariants-method locateVariants,GRanges,TxDb,PromoterVariants-method locateVariants,GRanges,TxDb,SpliceSiteVariants-method locateVariants,GRanges,TxDb,ThreeUTRVariants-method locateVariants,GRanges,TxDb,VariantType-method locateVariants,IntegerRanges,GRangesList,VariantType-method locateVariants,IntegerRanges,TxDb,VariantType-method locateVariants,VCF,GRangesList,VariantType-method locateVariants,VCF,TxDb,VariantType-method
PolyPhenDb objects	class:PolyPhenDb columns,PolyPhenDb-method duplicateRSID keys,PolyPhenDb-method metadata,PolyPhenDb-method PolyPhen PolyPhenDb PolyPhenDb-class select,PolyPhenDb-method
PolyPhenDb Columns	PolyPhenDbColumns
elementary vep/homo_sapiens/region call to ensembl VEP REST API	post_Hs_region
Predict amino acid coding changes for variants	predictCoding predictCoding,CollapsedVCF,TxDb,ANY,missing-method predictCoding,ExpandedVCF,TxDb,ANY,missing-method predictCoding,GRanges,TxDb,ANY,DNAStringSet-method predictCoding,IntegerRanges,TxDb,ANY,DNAStringSet-method predictCoding,VRanges,TxDb,ANY,missing-method
Convert posterior genotype probability to a SnpMatrix object	probabilityToSnpMatrix
PROVEANDb objects	class:PROVEANDb columns,PROVEANDb-method keys,PROVEANDb-method keytypes,PROVEANDb-method PROVEAN PROVEANDb PROVEANDb-class select,PROVEANDb-method
Read VCF files	import,VcfFile,ANY,ANY-method readGeno readGT readInfo readVcf readVcf,character,ANY-method readVcf,character,missing-method readVcf,TabixFile,GRanges-method readVcf,TabixFile,GRangesList-method readVcf,TabixFile,IntegerRangesList-method readVcf,TabixFile,missing-method readVcf,TabixFile,ScanVcfParam-method
Import VCF files	scanVcf scanVcf,character,missing-method scanVcf,character,ScanVcfParam-method scanVcf,connection,missing-method scanVcf,TabixFile,GRanges-method scanVcf,TabixFile,IntegerRangesList-method scanVcf,TabixFile,missing-method scanVcf,TabixFile,ScanVcfParam-method scanVcfHeader scanVcfHeader,character-method scanVcfHeader,missing-method scanVcfHeader,TabixFile-method
Parameters for scanning VCF files	ScanVcfParam ScanVcfParam,ANY-method ScanVcfParam,missing-method ScanVcfParam-class vcfFixed vcfFixed<- vcfGeno vcfGeno<- vcfInfo vcfInfo<- vcfSamples vcfSamples<- vcfTrimEmpty vcfTrimEmpty<- vcfWhich vcfWhich<-
Get seqinfo for VCF file	seqinfo seqinfo,VcfFile-method seqinfo,VcfFileList-method
SIFTDb objects	class:SIFTDb columns,SIFTDb-method keys,SIFTDb-method metadata,SIFTDb-method select,SIFTDb-method SIFT SIFTDb SIFTDb-class
SIFTDb Columns	SIFTDbColumns
Counts and distribution statistics for SNPs in a VCF object	snpSummary snpSummary,CollapsedVCF-method
Summarize variants by sample	summarizeVariants summarizeVariants,GRangesList,VCF,function-method summarizeVariants,GRangesList,VCF,VariantType-method summarizeVariants,TxDb,VCF,CodingVariants-method summarizeVariants,TxDb,VCF,FiveUTRVariants-method summarizeVariants,TxDb,VCF,IntronVariants-method summarizeVariants,TxDb,VCF,PromoterVariants-method summarizeVariants,TxDb,VCF,SpliceSiteVariants-method summarizeVariants,TxDb,VCF,ThreeUTRVariants-method
helper function to construct inputs for VEP REST API	variant_body
Defunct Functions in Package 'VariantAnnotation'	dbSNPFilter MatrixToSnpMatrix readVcfLongForm readVcfLongForm,character,character,missing-method readVcfLongForm,character,character,ScanVcfParam-method readVcfLongForm,character,missing,missing-method readVcfLongForm,TabixFile,character,GRanges-method readVcfLongForm,TabixFile,character,IntegerRangesList-method readVcfLongForm,TabixFile,character,missing-method readVcfLongForm,TabixFile,character,ScanVcfParam-method refLocsToLocalLocs refLocsToLocalLocs,GRanges,missing,GRangesList-method refLocsToLocalLocs,GRanges,TxDb,missing-method regionFilter restrictToSNV VariantAnnotation-defunct VRangesScanVcfParam
VariantType subclasses	AllVariants AllVariants-class CodingVariants CodingVariants-class downstream downstream,AllVariants-method downstream,IntergenicVariants-method downstream,PromoterVariants-method downstream<- downstream<-,AllVariants-method downstream<-,IntergenicVariants-method downstream<-,PromoterVariants-method FiveUTRVariants FiveUTRVariants-class idType idType,IntergenicVariants-method idType<- idType<-,IntergenicVariants-method intergenic intergenic,AllVariants-method intergenic<- intergenic<-,AllVariants-method IntergenicVariants IntergenicVariants-class IntronVariants IntronVariants-class promoter promoter,AllVariants-method promoter<- promoter<-,AllVariants-method PromoterVariants PromoterVariants-class show,AllVariants-method show,PromoterVariants-method show,VariantType-method SpliceSiteVariants SpliceSiteVariants-class ThreeUTRVariants ThreeUTRVariants-class upstream upstream,AllVariants-method upstream,IntergenicVariants-method upstream,PromoterVariants-method upstream<- upstream<-,AllVariants-method upstream<-,IntergenicVariants-method upstream<-,PromoterVariants-method VariantType-class
VCF class objects	alt alt,VCF-method alt<- alt<-,CollapsedVCF,CharacterList-method alt<-,CollapsedVCF,DNAStringSetList-method alt<-,ExpandedVCF,character-method alt<-,ExpandedVCF,DNAStringSet-method cbind,VCF-method class:CollapsedVCF class:ExpandedVCF class:VCF CollapsedVCF CollapsedVCF-class dimnames<-,VCF,list-method expand,CollapsedVCF-method expand,ExpandedVCF-method ExpandedVCF ExpandedVCF-class filt filt,VCF-method filt<- filt<-,VCF,character-method fixed fixed,VCF-method fixed<- fixed<-,VCF,DataFrame-method geno geno,VCF,ANY-method geno,VCF,character-method geno,VCF,numeric-method geno,VCF-method geno,VCFHeader,ANY-method geno<- geno<-,VCF,character,matrix-method geno<-,VCF,missing,matrix-method geno<-,VCF,missing,SimpleList-method geno<-,VCF,numeric,matrix-method genome,VCF-method genotypeCodesToNucleotides header,VCF-method header<- header<-,VCF,VCFHeader-method info info,VCF-method info<- info<-,VCF,DataFrame-method mcols<-,VCF,ANY-method mcols<-,VCF-method qual qual,VCF-method qual<- qual<-,VCF,numeric-method rbind,VCF-method ref ref,VCF-method ref<- ref<-,VCF,DNAStringSet-method rowRanges,VCF-method rowRanges<-,VCF,GRanges-method seqlevels,VCF-method show,CollapsedVCF-method show,ExpandedVCF-method show,VCF-method SnpMatrixToVCF strand,VCF-method strand<-,VCF,ANY-method subset,VCF-method updateObject,VCF-method VCF VCF-class vcfFields,VCF-method [,VCF,ANY,ANY,ANY-method [,VCF,ANY,ANY-method [,VCF-method [<-,VCF,ANY,ANY,VCF-method
Manipulate Variant Call Format (Vcf) files.	vcfFields,character-method vcfFields,missing-method vcfFields,VcfFile-method vcfFields,VcfFileList-method VcfFile VcfFile-class VcfFileList VcfFileList-class
VCFHeader instances	contig contig,VCFHeader-method fixed,VCFHeader-method fixed<-,VCFHeader,DataFrameList-method geno,VCFHeader-method geno<-,VCFHeader,missing,DataFrame-method header header,VCFHeader-method info,VCFHeader-method info<-,VCFHeader,DataFrame-method meta meta,VCFHeader-method meta<- meta<-,VCFHeader,DataFrame-method meta<-,VCFHeader,DataFrameList-method reference reference,VCFHeader-method samples samples,VCFHeader-method seqinfo,VCFHeader-method show,VCFHeader-method vcfFields vcfFields,VCFHeader-method VCFHeader VCFHeader-class
Use the VEP region API on variant information in a VCF object as defined in VariantAnnotation.	vep_by_region
VRanges objects	alt,VRanges-method alt<-,VRanges,ANY-method altDepth altDepth,VRanges-method altDepth<- altDepth<-,VRanges-method altFraction altFraction,VRanges-method asVCF asVCF,VRanges-method called called,VRanges-method characterOrRle-class characterRle-class class:VRanges coerce,GRanges,VRanges-method coerce,VCF,VRanges-method coerce,VRanges,VCF-method complexRle-class factorOrRle-class factorRle-class hardFilters hardFilters,VRanges-method hardFilters<- hardFilters<-,VRanges-method integerOrRle-class integerRle-class logicalRle-class makeVRangesFromGRanges match,VRanges,VRanges-method numericRle-class rawRle-class readVcfAsVRanges ref,VRanges-method ref<-,VRanges,ANY-method refDepth refDepth,VRanges-method refDepth<- refDepth<-,VRanges-method resetFilter sampleNames,VRanges-method sampleNames<-,VRanges,ANY-method softFilter softFilterMatrix softFilterMatrix,VRanges-method softFilterMatrix<- softFilterMatrix<-,VRanges-method tabulate tabulate,VRanges-method totalDepth totalDepth,VRanges-method totalDepth<- totalDepth<-,VRanges-method VRanges VRanges-class writeVcf,VRanges,ANY-method
VRangesList objects	alt,VRangesList-method class:CompressedVRangesList class:SimpleVRangesList class:VRangesList CompressedVRangesList-class ref,VRangesList-method SimpleVRangesList-class stackSamples stackSamples,VRangesList-method VRangesList VRangesList-class
Write VCF files	writeVcf writeVcf,VCF,character-method writeVcf,VCF,connection-method