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VariantAnnotation (version 1.18.5)
Annotation of Genetic Variants
Description
Annotate variants, compute amino acid coding changes, predict coding outcomes.
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Version
1.18.5
1.18.1
1.16.1
1.14.13
1.12.9
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Version
1.18.5
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
January 1st, 1970
Functions in VariantAnnotation (1.18.5)
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VariantAnnotation-defunct
Defunct Functions in Package
VariantAnnotation
isSNV
Identification of genomic variant types.
PolyPhenDb-class
PolyPhenDb objects
predictCoding
Predict amino acid coding changes for variants
PolyPhenDbColumns
PolyPhenDb Columns
filterVcf
Filter VCF files
genotypeToSnpMatrix
Convert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs
Get transcript sequences
locateVariants
Locate variants
GLtoGP
Convert genotype likelihoods to genotype probabilities
PROVEANDb-class
PROVEANDb objects
SIFTDbColumns
SIFTDb Columns
probabilityToSnpMatrix
Convert posterior genotype probability to a SnpMatrix object
readVcf
Read VCF files
snpSummary
Counts and distribution statistics for SNPs in a VCF object
scanVcf
Import VCF files
ScanVcfParam-class
Parameters for scanning VCF files
summarizeVariants
Summarize variants by sample
SIFTDb-class
SIFTDb objects
VariantType-class
VariantType subclasses
VcfFile
Manipulate Variant Call Format (Vcf) files.
VCF-class
VCF class objects
VCFHeader-class
VCFHeader instances
VRanges-class
VRanges objects
VRangesList-class
VRangesList objects
writeVcf
Write VCF files