benchmark: AML31 benchmarking tool

In genome/aml31Benchmarking: Benchmark variant calls against curated variant lists from aml31

Description

Takes a 5-column single-nucleotide variant list generated by running your favorite tool on the AML31 data. Produces some informative plots and statistics, along with a table listing which variants were valid in both the "Platinum" and "Gold" truth sets.

Usage

    benchmark(variants, tablePrefix, plotFile)

Arguments

variants	Data frame containing ingle nucleotide variants in 5-column format: 1) chromosome 2) start position 3) stop position, 4) reference allele 5) variant allele
plotFile	filename to which plots will be output (in PDF output)
tablePrefix	filename prefix to which labelled variants will be output (in tsv format). Two files will be created: <prefix>.gold and <prefix>.platinum

genome/aml31Benchmarking documentation built on May 17, 2019, 1:11 a.m.