Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.

CombineGVCFs warn messages into GVCF output??


I just switched to GATK 3.6 because of the bug in CombineGVCFs reported at http://gatkforums.broadinstitute.org/gatk/discussion/comment/31641#Comment_31641

I have noticed that now the CombineGVCFs outputs WARN messages in the end of the VCF, like:

Done. There were 102 WARN messages, the first 10 are repeated below.
WARN 16:26:46,730 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
WARN 16:26:46,733 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation

and so on. Which wasn't the case in the previous version. The rest of the VCF is well formed, but yet exit status
of the program is not zero, as an error has occurred. I don't know how to get rid of it, and why is it polluting the vcf and not the stdout/stderr
with such messages?

Thanks in advance,



Best Answer


  • beruttiberutti Member

    Sorry, I don't know why I did not get any notification back then about the answer! When I logged back in I received a popup! For completeness even if a long time passed by: there was an error in the wrapper script fror GATK that was redirecting stderr and stdout all together. So my fault!

Sign In or Register to comment.