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.bol...@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 > > ___________________________________________________________ > 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: > > http://galaxyproject.org/search/mailinglists/ > -- 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: http://galaxyproject.org/search/mailinglists/
