truvari_benchmark

[georgiakes]

The subworkflow uses bcftools_reheader to include the contigs and their lengths in the header.

However, I can see that in truvari 5.4 these elements are already included in the output. There are some test results in the repo what shows that.

Should we remove reheader? Should we keep reheader regardless? If we remove it then we cannot justify a subworkflow since we will have only one module.

I would love some feedback :) @kubranarci

[kubranarci]

If that is the case, the is no point to keep bcftools_reheader, and no subworkflow will be needed indeed :) It also seems like they perform multi-vcf benchmarking. I didnt deep further but that can be a nice feture to add the pipeline?

[georgiakes]

Nice! About the multi-vcfs, I'm not sure I understood. The pipeline already process multu-sample VCFs, right?

[kubranarci]

Sorry, what I meant was multi-sample VCFs. The pipeline supports benchmarking with multi sample VCFs but through subsampling them. I have to dig in a bit but I think truvari now supports benchmarking with multi-sample vcfs as well.