%variant_in% | Match variants by position and allele |
%variant_in%-method | Match variants by position and allele |
annotateWithControlDepth | Annotate Case with Control Depth |
calculateConcordanceMatrix | Variant Concordance |
calculateVariantConcordance | Variant Concordance |
callGenotypes | Call Genotypes |
callGenotypes-method | Call Genotypes |
CallGenotypesParam | Call Genotypes |
callSampleSpecificVariants | Call Sample-Specific Variants |
callSampleSpecificVariants-method | Call Sample-Specific Variants |
callVariantConcordance | Variant Concordance |
callVariants | Call Variants |
callVariants-method | Call Variants |
callWildtype | Calling Wildtype |
coverage_H1993 | Vignette Data |
coverage_H2073 | Vignette Data |
DepthFETFilter | Variant Filter Constructors |
extractCoverageForPositions | Get Coverage at Positions |
genome_p53 | Vignette Data |
matchVariants | Match variants by position and allele |
MaxControlFreqFilter | Variant Filter Constructors |
minCallableCoverage | Calling Wildtype |
MinTotalDepthFilter | Variant Filter Constructors |
p53 | Vignette Data |
pileupVariants | Nucleotide pileup from alignments |
postFilterVariants | Post-filtering of Variants |
qaVariants | QA Filtering of Variants |
SampleSpecificVariantFilters | Call Sample-Specific Variants |
SetdiffVariantsFilter | Variant Filter Constructors |
tallies_H1993 | Vignette Data |
tallies_H2073 | Vignette Data |
tallyVariants | Tally the positions in a BAM file |
tallyVariants-method | Tally the positions in a BAM file |
TallyVariantsParam | Tally the positions in a BAM file |
VariantCallingFilters | Call Variants |
variantGR2Vcf | Create a VCF for some variants |
VariantPostFilters | Post-filtering of Variants |
VariantQAFilters | QA Filtering of Variants |
VariantTallyParam | Tally the positions in a BAM file |