Hello! Loving Parabricks so far, incredibly helpful and easy to use.
In germline runs that include DeepVariant, I am looking for a way to output both (1) VCF and (2) gVCF from DeepVariant. I have not figured out a way to do this, and the AI docs helper claims I need to pick one or the other. When running outside of parabricks (using google container), this works without issue, as you may just explicitly set the outputs for each file and get both.
It is pretty helpful to get both, rather than only one without the other. How can I make this happen?
Older, unanswered post here: Output both VCF and gVCF when using deepvariant