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