BAM from GATK best practice

tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

GNU General Public License v2.0

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BAM from GATK best practice #82

Open sbgLuka opened 3 years ago

sbgLuka commented 3 years ago

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 commented 2 years ago

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.