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 najoshi@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.
galaxy-dev@lists.galaxyproject.org