.VAUtil-class           ".VAUtil" and potentially other related classes
                        - in progress
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
VAFilter-class          VAFilter objects - under construction
VAFilterResult-class    "VAFilterResult" for VAFilter output and
                        statistics
VCF-class               VCF instances
VCFHeader-class         VCFHeader instances
VariantType-class       VariantType subclasses
getTranscriptSeqs       Get transcript sequences
locateVariants          Locate variants
predictCoding           Predict amino acid coding changes for variants
readVcf                 Read VCF files
readVcfLongForm         Read VCF files into a long form GRanges
refLocsToLocalLocs      refLocsToLocalLocs
scanVcf                 Import VCF files
summarizeVariants       Summarize variants by sample
writeVcf                Write VCF files
