To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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

Sign In or Register to comment.