Tools for Exploratory Analysis of Variant Calls

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Documentation for package ‘VariantTools’ version 1.48.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

%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