github.com/broadinstitute/palantir-workflows/BenchmarkVCFs2

A workflow to calculate sensitivity and precision of a germline variant calling pipeline by comparing a ‘call’ vcf produced by the pipeline to a gold standard ‘truth’ vcf. Allows for stratification based on interval lists, bed files, or variant types defined according to GATK SelectVariants.


This is a companion discussion topic for the original entry at github.com/broadinstitute/palantir-workflows/BenchmarkVCFs2