# Tools for Exploratory Analysis of Variant Calls

## Documentation for package ‘VariantTools’ version 1.22.0

- 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