Man pages for VariantAnnotation
Annotation of Genetic Variants

defunctDefunct Functions in Package 'VariantAnnotation'
filterVcf-methodsFilter VCF files
genotypeToSnpMatrix-methodsConvert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs-methodsGet transcript sequences
GLtoGPConvert genotype likelihoods to genotype probabilities
indexVcf-methodCreate index files for VCF files
isSNV-methodsIdentification of genomic variant types.
locateVariants-methodsLocate variants
PolyPhenDb-classPolyPhenDb objects
PolyPhenDbColumnsPolyPhenDb Columns
predictCoding-methodsPredict amino acid coding changes for variants
probabilityToSnpMatrixConvert posterior genotype probability to a SnpMatrix object
PROVEANDb-classPROVEANDb objects
readVcf-methodsRead VCF files
scanVcf-methodsImport VCF files
ScanVcfParam-classParameters for scanning VCF files
seqinfo-methodGet seqinfo for VCF file
SIFTDb-classSIFTDb objects
SIFTDbColumnsSIFTDb Columns
snpSummaryCounts and distribution statistics for SNPs in a VCF object
summarizeVariants-methodsSummarize variants by sample
VariantType-classVariantType subclasses
VCF-classVCF class objects
VcfFile-classManipulate Variant Call Format (Vcf) files.
VCFHeader-classVCFHeader instances
VRanges-classVRanges objects
VRangesList-classVRangesList objects
writeVcf-methodsWrite VCF files
VariantAnnotation documentation built on Nov. 8, 2020, 5:08 p.m.