VariantAnnotation: Annotation of Genetic Variants

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

Author
Valerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]
Date of publication
None
Maintainer
Valerie Obenchain <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.20.2

View on Bioconductor

Man pages

defunct
Defunct Functions in Package 'VariantAnnotation'
filterVcf-methods
Filter VCF files
genotypeToSnpMatrix-methods
Convert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs-methods
Get transcript sequences
GLtoGP
Convert genotype likelihoods to genotype probabilities
isSNV-methods
Identification of genomic variant types.
locateVariants-methods
Locate variants
PolyPhenDb-class
PolyPhenDb objects
PolyPhenDbColumns
PolyPhenDb Columns
predictCoding-methods
Predict amino acid coding changes for variants
probabilityToSnpMatrix
Convert posterior genotype probability to a SnpMatrix object
PROVEANDb-class
PROVEANDb objects
readVcf-methods
Read VCF files
scanVcf-methods
Import VCF files
ScanVcfParam-class
Parameters for scanning VCF files
SIFTDb-class
SIFTDb objects
SIFTDbColumns
SIFTDb Columns
snpSummary
Counts and distribution statistics for SNPs in a VCF object
summarizeVariants-methods
Summarize variants by sample
VariantType-class
VariantType subclasses
VCF-class
VCF class objects
VcfFile-class
Manipulate Variant Call Format (Vcf) files.
VCFHeader-class
VCFHeader instances
VRanges-class
VRanges objects
VRangesList-class
VRangesList objects
writeVcf-methods
Write VCF files

Files in this package

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