API for Bioconductor-mirror/VariantTools
Tools for Exploratory Analysis of Variant Calls

Global functions
AverageNeighborCountFilter Source code
BinomialLRFilter Source code
CallGenotypesParam Man page Source code
CallableInOtherFilter Source code
DepthFETFilter Man page Source code
DistanceToNearestFilter Source code
GenotypeRunVRanges Source code
IndelsNotSupportedFilter Source code
InternalReadPosBinFilter Source code
LowerFrequencyInOtherFilter Source code
MaskFilter Source code
MaxControlFreqFilter Man page Source code
MedianDistFromNearestEndFilter Source code
MinAltDepthFilter Source code
MinTotalDepthFilter Man page Source code
NeighborCountFilter Source code
NonNRefFilter Source code
NonRefFilter Source code
ReadPosCountFilter Source code
ReadPositionTTestFilter Source code
SampleSpecificVariantFilters Man page Source code
SetdiffPositionsFilter Source code
SetdiffVariantsFilter Man page Source code
SingleVariantFilter Source code
StrandFETFilter Source code
TallyVariantsParam Man page Source code
VariantCallingFilters Man page Source code
VariantConcordanceFilters Source code
VariantPostFilters Man page Source code
VariantQAFilters Man page Source code
VariantSanityFilters Source code
VariantTallyParam Man page
\%variant_in\% Man page
\%variant_in\%,GenomicRanges,GenomicRanges-method Man page
addGenotypeRuns Source code
annotateWithControlDepth Man page Source code
calculateConcordanceMatrix Man page Source code
calculatePowerInOther Source code
calculateVariantConcordance Man page Source code
callGenotypes Man page
callGenotypes,TabixFile-method Man page
callGenotypes,VRanges-method Man page
callGenotypesOneRegion Source code
callSampleSpecificVariants Man page
callSampleSpecificVariants,BamFile,BamFile-method Man page
callSampleSpecificVariants,GenomicRanges,GenomicRanges-method Man page
callSampleSpecificVariants,VRanges,VRanges-method Man page
callSampleSpecificVariants,character,character-method Man page
callVariantConcordance Man page Source code
callVariants Man page
callVariants,BamFile-method Man page
callVariants,GenomicRanges-method Man page
callVariants,VRanges-method Man page
callVariants,character-method Man page
callWildtype Man page Source code
caseControlFET Source code
chunkRange Source code
codon2trans Source code
compute_GL Source code
compute_GQ Source code
compute_GT Source code
coverage_H1993 Man page
coverage_H2073 Man page
defaultBPPARAM Source code
extractCoverageForPositions Man page Source code
file_ext_sans_gz Source code
findAverageNeighborCount Source code
fisher_p Source code
fisher_p_vectorized Source code
flankingCycleBreaks Source code
genome_p53 Man page
getConcordantCliques Source code
installed Source code
loadAndComputeGenotypesForRegion Source code
loadVariants Source code
lrtFreqCutoff Source code
matchVariants Man page Source code
mergeVariantInfo Source code
minCallableCoverage Man page Source code
p53 Man page
phred Source code
pileupGRanges Source code
pileupGRangesOverGenome Source code
pileupVariants Man page Source code
postFilterVariants Man page Source code
qaVariants Man page Source code
rawTotalDepth Source code
sanitizeVariants Source code
t.test_welch Source code
tallies_H1993 Man page
tallies_H2073 Man page
tallyVariants Man page
tallyVariants,BamFile-method Man page
tallyVariants,BamFileList-method Man page
tallyVariants,character-method Man page
test Source code
trans2genome Source code
twoWayTabulate Source code
valid_TallyVariantsParam Source code
variantGR2Vcf Man page Source code
variantKeys Source code
variant_intersect Source code
variant_setdiff Source code
Bioconductor-mirror/VariantTools documentation built on June 1, 2017, 3:28 a.m.