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VariantTools (version 1.14.1)

Tools for Working with Genetic Variants

Description

Tools for detecting, filtering, calling, comparing and plotting variants.

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Version

Version

1.14.1

License

Artistic-2.0

Maintainer

Michael Lawrence

Last Published

February 15th, 2017

Functions in VariantTools (1.14.1)

variantGR2Vcf

Create a VCF for some variants
extractCoverageForPositions

Get Coverage at Positions
pileupVariants

Nucleotide pileup from alignments
tallyVariants

Tally the positions in a BAM file
callWildtype

Calling Wildtype
postFilterVariants

Post-filtering of Variants
callSampleSpecificVariants

Call Sample-Specific Variants
matchVariants

Match variants by position and allele
callGenotypes

Call Genotypes
callVariants

Call Variants
concordance

Variant Concordance
annotateWithControlDepth

Annotate Case with Control Depth
qaVariants

QA Filtering of Variants
FilterConstructors

Variant Filter Constructors