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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: http://gatkforums.broadinstitute.org/gatk/discussion/7743/bug-with-version-3-6-and-jexl

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.



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