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.
Errors on the road to GATK
I am using the best practices RNA-Seq pipeline for 6 libraries. Four have completed without any problem. Two (from the same project) have gotten snagged. The errors occur at "add or replace read groups" and at "mark duplicates." The errors:
Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Read name HWI-D00273:94:C6GFHANXX:8:1312:12804:32959, CIGAR M operator maps off end of reference
Exception in thread "main" net.sf.samtools.SAMFormatException: Did not inflate expected amount
I know picard tools is not part of GATK, but wondered if anyone has thoughts about what's going on. I have tried starting from scratch with trimmed reads, running cleansam, checking that all pairs are intact...nothing helps. I'm especially puzzled that the other libraries have no issues.