One of my co-administrators is having some issues with data
indexed/processed with data managers in GATK. His email to me:
Currently there is no way to load a genome into versions of GATK above
version 1.4. No version seems to be able to load a reference from history
and only version 1.4 seems to work with the available picard-gatk data
manager. We need to be able to work with these later versions of GATK, 3.4
on the Galaxy tool shed is the latest.
Has anyone else experienced this sort of issue? Is there some solution for
Scott B. Szakonyi
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
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