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

MarkDuplicatesWithMateCigar fails at producing metrics files with some samples


With most of my samples, MarkDuplicatesWithMateCigar works just fine. For some however, while it runs for the same amount of time and seem to behave similarly, it fails at producing the metrics file and tells me that: "Exception in thread "main" picard.PicardException: Found a samRecordWithOrdinal with sufficiently large clipping that we may have missed including it in an early duplicate marking iteration. Please increase the minimum distance to at least 252bp to ensure it is considered (was 252)." What should I do?


Best Answer


  • benjaminpelissiebenjaminpelissie Madison, WIMember

    Thank you @Geraldine_VdAuwera. My apologies, I didn't notice the MINIMUM_DISTANCE option in MarkDuplicatesWithMateCigar (don't know why). I'll go with MarkDuplicates anyway, as you advised me already.

Sign In or Register to comment.