Looking for GPU Benchmarking

[kuhnsa3]

I have some benchmarking information using different allocations of A100 GPUs here for the parabrick’s germline workflow:

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…

Have you benchmarked any of the germline workflows (either GATK or deepvariant) against the GIAB samples? I am seeing very low recall with parabricks when compared to the tools available from The Broad or Google.