BAM from GATK best practice

[sbgLuka]

Hi, I know that there is a section which says that BAM file should be used from BWA MEM, but does this mean that we could also use BAM file created by GATK best practice workflow, which means that BAM is deduplicated and bases are recalibrated? Or we should use BAM straightforward from BWA?

Thanks,
Luka!

[aubreybailey]

I would think this shouldnt matter, except in stutter correction. The stutter correction profile is probably "good enough" even if you dont have enough samples to build your own model, but if you -do- have enough then the model will learn either way.