In past versions of GATK, I have found using -nct option to make haplotype caller non-deterministic in nature.
Is this still the case or do you now suggest using the -nct flag to add threads to speed up variant detection?
That has not changed, and also applies to MuTect2. We use scatter gather parallelism to speed up this step in the pipeline.
@Geraldine_VdAuwera: Thanks as always for the information!