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Great, thanks Sheila. We'll try it out.
FWIW no_pg_tag didn't help me either; changing the header was the only thing that worked. A bit of a pain, but I only had to do it a few times before I got convergence on my call-snps-recalibrate-call-snps-recalibrate loop.
It does have two @PG PrintReads entries. They're identical and each reads as follows: (Quote) I'm using samtools to remove these lines from the header and I'll try to run UnifiedGenotyper again, then report back.
Hi Dr. Carneiro, I saw the error running UnifiedGenotyper.
Update Received same error message using v2.4-9 ... I'll try using --no_pg_tag. Thanks for your help!
Hi Dr. Van der Auwera, Oops, I was running v2.4-7. (I'm not sure how that happened; I've only been doing this for a couple of weeks.) I will upgrade and retry, then post results. Thanks!