Genotypes-class         Genotypes class objects
TVTB-package            TVTB: The VCF Tool Box
TVTBparam-class         TVTBparam class objects
VcfFilterRules-class    VcfFilterRules class objects
addCountGenos-methods   Add count of genotypes to INFO field
addFrequencies-methods
                        Group-level genotypes counts and allele
                        frequencies
addOverallFrequencies-methods
                        Overall genotypes counts and allele frequencies
addPhenoLevelFrequencies-methods
                        Genotypes and allele frequencies for a given
                        phenotype level
autodetectGenotypes-methods
                        Define genotypes in the TVTBparam metadata slot
class:VcfFixedRules     VCF filters class objects sub-types
countGenos-methods      Count occurences of genotypes
dropInfo-methods        Remove INFO keys from VCF objects
pairsInfo-methods       Plot an INFO metric on a genomic axis.
parseCSQToGRanges       Parse the CSQ column of a VCF object into a
                        GRanges object
plotInfo-methods        Plot an INFO metric on a genomic axis.
readVcf,character,TVTBparam-method
                        Read VCF files
tSVE                    The Shiny Variant Explorer (tSVE)
                        web-application
variantsInSamples-methods
                        Identify variants observed in samples
vepInPhenoLevel-methods
                        VEP predictions of variants observed in samples
