Comments (1)
I tried rerunning with GATK 4.5.0.0 which has Picard 3.1.1 and HTSJDK 4.1.0 and it finished successfully. I'm going to assume this was either an old version bug or a very weird transient edge case. I'm not invested enough to try to rerun it and see which of the two it was, but feel free to reopen if anyone wants to investigate this further.
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Related Issues (20)
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