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Question: Gatk - Base Recalibrator
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gravatar for Bolduc, Francois
4.8 years ago by
Bolduc, Francois • 10
Bolduc, Francois • 10 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
gatk • 1.5k views
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modified 4.8 years ago by Geraldine Van der Auwera • 40 • written 4.8 years ago by Bolduc, Francois • 10
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gravatar for Geraldine Van der Auwera
4.8 years ago by
Geraldine Van der Auwera • 40
United States
Geraldine Van der Auwera • 40 wrote:
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 < -- Geraldine A. Van der Auwera, Ph.D. Bioinformatics Scientist Broad Institute
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