Dear Everyone!
We have recently switched to NVIDIA Parabricks for our germline variant calling pipeline, however we have trouble with variant calling on the Y chromosome.
Unfortunately I can only see the –haploid-contigs setting, but I do not see a setting where I could set which regions of the Y and X chromosomes are diploid.
Google DeepVariant provides a parameter called –par_regions_bed. Is there a way to set it in Parabricks?
Thank you for helping in advance!
Best Regards,