Heys,

I'm trying to run GATK on some BAM files I got. When I try, I obtain this error message:

A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file.

But when I check for the Read Group, is missing. Moreover, when I try to add a Read Group with AddOrReplaceReadGroup, the file gets truncated, with this error message:

SAM validation error: ERROR::INVALID_MAPPING_QUALITY:Record 55, Read name SRR836354.49744060, MAPQ should be 0 for unmapped read.

Do you know how can I check the different samples I have within this BAM or how could I specify the Read Group?

Thanks in advance!