Change in the Range of Values Between DRAGEN 2.6+ and Earlier Versions of DRAGEN/GATK

The range of the QUAL (and therefore GQ and QD) values has changed between older DRAGEN versions (and/or GATK) and DRAGEN 2.6 and later versions. In older DRAGEN versions, the QUAL calculations followed the GATK approach. In newer DRAGEN versions (2.6 and later), the algorithms for small variant detection were improved and they result in more realistic QUAL (and therefore GQ and QD) values (ie, smaller values than GATK).

The QUAL values changed because the probability calculations used by GATK and earlier DRAGEN versions assume that errors are uncorrelated across reads. This is assumed for both mapping errors and base-call errors. In a real world with correlated errors, this leads to wildly inflated QUAL scores as well as suboptimal detection performance. The algorithms in DRAGEN 2.6 and later incorporate the hypothesis of correlated errors from within the variant caller, leading to more accurate detection and more realistic QUAL scores. The more realistic QUAL scores in DRAGEN 2.6+ are smaller than the inflated QUAL scores in GATK.