Hello,

I am working on it; I already integrate some tools of GATK3 in a dedicated instance of galaxy;


-> RealignerTargetCreator <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_RealignerTargetCreator.html> -> IndelRealigner <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_IndelRealigner.html> -> HaplotypeCaller <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html>

These are the tools that I use most; I have written the wrappers in java ...

I need at least one or two more week to achieve a package that could be published in a tool shed (for testing)

Florian


-------- Message original --------
Sujet:  [galaxy-dev] genotypeGVCFs in galaxy from GATK 3.0
Date :  Tue, 20 May 2014 17:25:55 -0700
De :    Nikhil Joshi <najo...@ucdavis.edu>
Pour :  galaxy-dev@lists.bx.psu.edu <galaxy-dev@lists.bx.psu.edu>



Hi all,

Is anyone working on (or has already created) wrappers for GATK 3.0? Specifically, I'm looking for a wrapper for genotypeGVCFs, but it seems like I would want all the GATK wrappers to be updated. Any help is highly appreciated!

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)




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