[galaxy-dev] Issue with GATK2 on Galaxy Repository.

Hi Dev, I am running a local instance Galaxy for developing a variant calling pipeline. I ran into this issue after configuring and installing GATK2 on my local when running the GATK *Realigner Target Creator on the BAM file generated by Mark duplicates.* *Can some suggest how to resolve this issu

Re: [galaxy-dev] Issue with GATK2 on Galaxy Repository.

Hi, can you please check the exact version of the GATK jar file? Currently, only 2.8 is supported. We stopped maintaining it, due to licensing issues - which might be resolved in a 4.0 version. If you have GATK2.8, it should work hopefully. Cheers, Bjoern Am 31.05.2017 um 05:36 schrieb OLABODE O

Re: [galaxy-dev] Issue with GATK2 on Galaxy Repository.

Hi, which version of GATK are you using? From your email it seems you may be using GATK3, which is not supported by the Galaxy GATK2 wrappers. Cheers, Nicola On 31/05/17 04:36, OLABODE OLUWASEUN AJAYI wrote: Hi Dev, I am running a local instance Galaxy for developing a variant calling pipel