Qempirical and recalibrated quality score recal
I read the GATK paper, “A framework for variation discovery and genotyping using next-generation DNA sequencing data”.
In the ONLINE METHODS- Base quality score recalibration section, I understand the calculation of Qempirical(R,C,D). At this point, we’ve already get a recalibrated quality score, why we need to go further to get recal(r,c,d)? what’s the difference between “R,C,D” set and “r,c,d” set? The former is a superset of the latter?