Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?