Hi Frank, 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. Good luck Geraldine On Fri, Jan 31, 2014 at 1:51 PM, Bolduc, Francois < Francois.Bolduc@usherbrooke.ca> wrote:

Hi all,

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.

Frank

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