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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