I am trying to annotate the QD value in the Sparse Matrix Table(SMT) combining gVCFs using run_combiner(). As I know, the QD value can be calculated with QUAL / DP (or AD). By the way, I can see the RGQ value in SMT instead of the QUAL value in individual gVCFs. Please let me know how I interpret the RGQ value.
In addition, if you have some idea for getting QD value (Entry level or Site level).