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CIGAR operator format violation in ReducedBAMs?

MonkolMonkol BostonMember, Broadie

Hi

When running Picard on reduced BAMs, I get the following error message:
Ignoring SAM validation error: ERROR: Read name 18889, No real operator (M|I|D|N) in CIGAR

Are there any consequences of using "VALIDATION_STRINGENCY=LENIENT" and just ignoring these format violations?

Thanks!

Answers

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