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. Borrowed and adapted from the Broad Institute’s Hydrogen/Palantir repo, courtesy of Michael Gatzen (palantir-workflows/BenchmarkVCFs at mg_benchmark_compare · broadinstitute/palantir-workflows · GitHub ; permalink:
This is a companion discussion topic for the original entry at github.com/broadinstitute/long-read-pipelines/BenchmarkVCFsSmall