Yup, exactly. The old code was trying to use the same logic as GATK 1.6, but the Bayesian approach is  both more principled/correct *and* now gets >99.99% concordance with GATK.

I'm not sure why we get lower concordance when using GATK 1.6's logic, but I'm guessing it's because of two effects: a) their complicated logic basically reduces to the same as ours, and b) I didn't reproduce some aspect of their formula accurately.