Yes, that's equivalent; BaseRecalibrator is a single tool that combines
those two steps in more recent versions. The version of GATK in Galaxy (1.6
afaik) is a pretty old one. I would strongly recommend using the most
recent version of GATK (2.8) as it will give you better results.
On Fri, Jan 31, 2014 at 1:51 PM, Bolduc, Francois <
I'm trying to call variants using GATK best practices workflow. So after
performing Realigner Target Creator step, one should jump on Base
Recalibrator step. Unfortunatly, I don't see this program under GATK tab.
Is there a way to perform this step in Galaxy?
There are the Count covariates and Table recalibration steps. Is a
combination of these two steps is equivalent to Base recalibrator?
Thank you for your help and time.
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