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.

Invalid JEXL expression detected

shanzorshanzor canberraMember


I am attempting to filter a combined vcf file with 400 samples based on several FORMAT fields in gatk 3.6.0 (latest overnight update). I have previously achieved this step with a different data set in an earlier version of gatk without issue. However now when using data processed in 3.6 I find I am getting an error, but only when I include a JEXL argument for the DP field, GQ for instance seems to work fine. The error is as follows:

MESSAGE: Invalid JEXL expression detected for low_cov with message no message.

I have checked the forum and there was a recent post that dealt with a bug in 3.6 that apparently caused a similar JEXL error, here:

This bug was apparently fixed, but I am using the most recent update of 3.6, so am not sure why I am getting the same problem?

Any advice greatly appreciated.



Sign In or Register to comment.