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Hi Shlee, After a bit of digging around I've found that it was the bam files that were the problem. I'm adding custom tags to the reads during alignment, and apparently these don't get on well with Mutect2. I've realigned with bwa and the run compl…
Hi Shlee, Actually, the original file I was using did not validate with ValidateSamFile (Mate not found for paired read), but I have since tried with BAMs that pass ValidateSamFile, and get the same error as above: INFO 15:37:09,306 HelpFormatter…
I have the same problem - did you manage to fix this?