the standard deepvariant tool can output both VCF and gVCF for the same sample at the end of variant calling. This is often quite convenient to compute stats on the regular VCF while having the gVCF for subsequent cohort merging.
The standard tool also generates an HTML QC report.
Is it possible to have the same outputs when running deepvariant in clara parabricks? Especially, can we have the VCF and gVCF simultaneously? It would be great to have the HTML report as well, but this is not essential.
So far, I’ve tried various combinations of --out-variants and --gvcf but I can only get variants in one of the 2 formats, but not both.