I found that the GATK tools do not have the same requirement tag. For
example indel-realigner has version 1.4, realigner_target_creator has
version 1.3. Is that correct? What is the recent version that is
required for GATK?
Also realigner_target_creator uses the "gatk_picard_indexes" location
file, but under tool-data is only a gatk_sorted_picard_indexes.loc
Are there any concrete plans for the GATK wrappers. Especially to update
to a newer version. Or is that not feasible because of this complicated
license policy and the phone-home option ...
I found the following trello card, but its a little bit outdated:
Is anyone running a recent GATK version in Galaxy?
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