GLtoGP                  Convert genotype likelihoods to genotype
                        probabilities
MatrixToSnpMatrix       Convert genotype calls from a VCF file to a
                        SnpMatrix object
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
VariantType-class       VariantType subclasses
filterVcf               Filter VCF files
genotypeToSnpMatrix     Convert genotype calls from a VCF file to a
                        SnpMatrix object
getTranscriptSeqs       Get transcript sequences
locateVariants          Locate variants
predictCoding           Predict amino acid coding changes for variants
probabilityToSnpMatrix
                        Convert posterior genotype probability to a
                        SnpMatrix object
readVcf                 Read VCF files
readVcfLongForm         Read VCF files into a long form GRanges
refLocsToLocalLocs      refLocsToLocalLocs
scanVcf                 Import VCF files
snpSummary              Counts and distribution statistics for SNPs in
                        a VCF object
summarizeVariants       Summarize variants by sample
writeVcf                Write VCF files
