GATK - Base recalibrator

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GATK - Base recalibrator

Bolduc, Francois
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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Re: GATK - Base recalibrator

Geraldine Van der Auwera
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 <[hidden email]> 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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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--
Geraldine A. Van der Auwera, Ph.D.
Bioinformatics Scientist
Broad Institute

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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