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