If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Foolproof way to get reads which will pass Picard, without losing too many
Ok, after some time away, we are getting back to writing a remapping tool that can handle lots of different cases. The protocol suggested by the Broad is good, but fails in cases when the bam had previous issues (weird read groups, weird read names, etc.), so we are doing it from scratch.
My issue now is that we are getting the following error A LOT:
Exception in thread "main" picard.PicardException: Adjacent reads expected to be mate-pairs have different names:
This occasionally happens even after running FixMateInformation (or the opposite error, two reads with the same name but not marked as a mate-pair)
I'm at the point where after doing all the cleaning steps (CleanSam, FixMateInformation...) I just want to throw out any read that is going to throw an exception for a downstream tool (in Picard and the GATK), but of course, I don't want to throw out anything else. Is
samtools view -f 2 -b mybam.bam > mybam_that_will_not_fail.bam going to work? Is it too restrictive? Is there another approach you would suggest to get my bams in shape?