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[kuhnsa3]

Would these bug fixes address the low recall that was observed here?

Very low Recall for HG002 germline benchmark

Is there anyone on NIVIDA’s side that can look into this? This seems like a potential issue with the tool that may need to be resolved. Have you benchmarked parabricks germline callers against any of the GIAB samples using hap.py? This is much lower than I would have expected. If I run a vanilla GATK germline workflow (using The Broad’s GATK) against the same input, I am seeing higher recall (see screen shot below). I also benchmarked the parabricks deepvariant germline caller and its performan…

I would love to use parabricks as the run times are fantastic but it is missing/not-calling a lot of variants.