This is a more generalised question. I wish to discover variants in my raw WGS data which has been produced by studies carried out by Broad Institute. What modifications would you recommend for the standard GATK best practices workflow to better suit Broad-produced data ?
For e.g., while GATK/Broad strongly recommends recalibrating base qualities, this workshop says at the end that
All recent Broad‐produced data is already recalibrated