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Error with SamTools in GATK 4 CNV Proportional Coverage

WillGibsonWillGibson Broad InstituteMember

Hi, I am attempting to run the GATK4 CNV Proportional Coverage task, but an error occurred in one of my samples. I've attached the stderr file. The relevant part seems to be there is an issue in a pointer in SAMtools I think. I found a discussion on a similar error on the GATK forums, http://gatkforums.broadinstitute.org/gatk/discussion/1668/depthofcoverage-error
but I'm not sure if it applies to this situation. I was wondering if you know how to fix this error?

Thanks for your help,
Will

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