I’m analyzing >200 human exomes following GATK Best Practices. I’ve tried to read all the GATK documentation about this, but I’d like to ask you something just to be sure. I understand that it is recommended using VQSR instead of hard filtering. I used the option --truth-sensitivity-filter-level 99.0 in ApplyVQSR, and in the end, I kept only the variants that had the PASS filter. I would like to confirm if I should apply any more filters (like QD<2) to make sure I don’t have any false positives.
Thank you in advance