A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchmark datasets). The workflow uses a combination of bedtools, mosdepth, rtg-tools, pandas and datavzrd.
The usage of this workflow is described in the Snakemake Workflow Catalog.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) benchmark-giabsitory and its DOI (see above).