SetdiffVariantsFilter   Variant Filter Constructors
annotateWithControlDepth
                        Annotate Case with Control Depth
calculateConcordanceMatrix
                        Variant Concordance
callGenotypes           Call Genotypes
callSampleSpecificVariants
                        Call Sample-Specific Variants
callVariants            Call Variants
callWildtype            Calling Wildtype
extractCoverageForPositions
                        Get Coverage at Positions
matchVariants           Match variants by position and allele
pileupVariants          Nucleotide pileup from alignments
postFilterVariants      Post-filtering of Variants
qaVariants              QA Filtering of Variants
tallies_H1993           Vignette Data
tallyVariants           Tally the positions in a BAM file
variantGR2Vcf           Create a VCF for some variants
