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 it?