Thanks for providing the variantbenchmarking pipeline, which I have run without problem. I am unsure how to interpret the various upset plots and wonder if there is a descriptive document somewhere. Thanks.

Hello! Sorry for the delayed answer, I was on a long holiday.. I think I forgot to add those, but nice call, I will do it soon as possible. Upset plots are mainly to compare common vs unique set of variants between multiple queries (TP_comp vs FP and TP_base vs FN). TP_comp, TP_base, FP and FN calls from the benchmark outputs are being collected to merge separately, and then upset plot uses those tables to plot the differences. https://github.com/nf-core/variantbenchmarking/blob/master/subworkflows/local/compare_benchmark_results/main.nf