Histogram of QUAL, QD, and GQ

When plotting the histogram of QUAL (and QD and GQ) values across the calls of a DRAGEN 2.6+ VCF, a peak can occur at a certain value (eg, 50) with a smaller portion of QUAL values below and above this level. This is because the Foreign Read Detection (FRD) algorithm sets a limit on the QUAL (and indirectly on GQ and QD) value of heterozygous variants. See Foreign Read Detection. The exact value depends on the mapping between the maximum MAPQ from the mapper and a phred confidence that a read is correctly mapped. Homozygous variants are not subject to this limit, because the FRD hypothesis is applied against heterozygous variants only (this in turn is because the --vc-frd-beta-max option that specifies the maximum allele frequency for the foreign read hypothesis is set to 0.5).

The high-level summary is that the QUAL of heterozygous variants is bounded, and the QUAL of homozygous variants is not. However, the QUAL scale is the same across all variants (het or hom), only the bound is different.