Hi team, I have a basic question, sorry. I am trying to use HaplotypeCaller and VariantRecalibrator with QUEUE but I don't know how add:
VariantRecalibrator.mode = BOTH
HaplotypeCaller.genotyping_mode = DISCOVERY
I get a "not found: value BOTH/DISCOVERY" error.
Thank you in advance,
For exome-sequencing, I was wondering how I should decide the "-mode" parameter? should I use "SNP" or "Indel" or both? I want to get both information in the final results, should I use "BOTH" -mode?