We have indexed a genome using the appropriate data manager, for GATK, and
our reference is showing up and working for individual walkers in GATK
2.8. When designing a workflow, however, the reference genome is not
appearing as an option for many walkers, including indel realigner and
realigner target creator. It is appearing for haplotype caller. Again
outside of the workflow environment the indexed references show up for all
Any thoughts on this issue?
Scott B. Szakonyi
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
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