%variant_in%	matchVariants
%variant_in%,GenomicRanges,GenomicRanges-method	matchVariants
annotateWithControlDepth	annnotateWithControlDepth
calculateConcordanceMatrix	concordance
calculateVariantConcordance	concordance
callGenotypes	callGenotypes
callGenotypes,TabixFile-method	callGenotypes
callGenotypes,VRanges-method	callGenotypes
CallGenotypesParam	callGenotypes
callSampleSpecificVariants	callSampleSpecificVariants
callSampleSpecificVariants,BamFile,BamFile-method	callSampleSpecificVariants
callSampleSpecificVariants,character,character-method	callSampleSpecificVariants
callSampleSpecificVariants,GenomicRanges,GenomicRanges-method	callSampleSpecificVariants
callSampleSpecificVariants,VRanges,VRanges-method	callSampleSpecificVariants
callVariantConcordance	concordance
callVariants	callVariants
callVariants,BamFile-method	callVariants
callVariants,character-method	callVariants
callVariants,GenomicRanges-method	callVariants
callVariants,VRanges-method	callVariants
callWildtype	callWildtype
coverage_H1993	vignette
coverage_H2073	vignette
DepthFETFilter	FilterConstructors
extractCoverageForPositions	extractCoverageForPositions
genome_p53	vignette
matchVariants	matchVariants
MaxControlFreqFilter	FilterConstructors
minCallableCoverage	callWildtype
MinTotalDepthFilter	FilterConstructors
p53	vignette
pileupVariants	pileupVariants
postFilterVariants	postFilterVariants
qaVariants	qaVariants
SampleSpecificVariantFilters	callSampleSpecificVariants
SetdiffVariantsFilter	FilterConstructors
tallies_H1993	vignette
tallies_H2073	vignette
tallyVariants	tallyVariants
tallyVariants,BamFile-method	tallyVariants
tallyVariants,BamFileList-method	tallyVariants
tallyVariants,character-method	tallyVariants
TallyVariantsParam	tallyVariants
VariantCallingFilters	callVariants
variantGR2Vcf	variantGR2Vcf
VariantPostFilters	postFilterVariants
VariantQAFilters	qaVariants
VariantTallyParam	tallyVariants
