I am trying to run VariantFiltration using a genotype filter on DP. This works in 3.5; however, with 3.6 it throws a rather uninformative error (stacktrace below). The command is something like:
java -jar GenomeAnalysisTK.jar \
-T VariantFiltration \
-R genome.fasta \
-V input.vcf.gz \
-o test.vcf.gz \
--setFilteredGtToNocall \
-G_filterName GQ-LT30 \
-G_filter 'DP < 30'
In 3.5 this works as expected. In 3.6 it gives the error below. Related genotype filters (like GQ < 20) work in 3.6, so this appears to be something specific to some attributes. There wasnt anything obvious in the code i could see to explain this. Stacktrace here:
29 Sep 2016 16:29:13,733 DEBUG: ##### ERROR --
29 Sep 2016 16:29:13,789 DEBUG: ##### ERROR stack trace
29 Sep 2016 16:29:13,944 DEBUG: java.lang.IllegalArgumentException: Invalid JEXL expression detected for DP-LT10 with message no message
29 Sep 2016 16:29:14,012 DEBUG: at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:136)
29 Sep 2016 16:29:14,143 DEBUG: at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:93)
29 Sep 2016 16:29:14,181 DEBUG: at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:22)
29 Sep 2016 16:29:14,341 DEBUG: at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:323)
29 Sep 2016 16:29:14,445 DEBUG: at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:433)
29 Sep 2016 16:29:14,607 DEBUG: at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:349)
29 Sep 2016 16:29:14,687 DEBUG: at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:97)
29 Sep 2016 16:29:14,741 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
29 Sep 2016 16:29:14,812 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
29 Sep 2016 16:29:14,887 DEBUG: at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
29 Sep 2016 16:29:14,935 DEBUG: at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
29 Sep 2016 16:29:15,008 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
29 Sep 2016 16:29:15,054 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
29 Sep 2016 16:29:15,315 DEBUG: at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
29 Sep 2016 16:29:15,417 DEBUG: at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
29 Sep 2016 16:29:15,694 DEBUG: at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
29 Sep 2016 16:29:15,785 DEBUG: at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
29 Sep 2016 16:29:15,883 DEBUG: at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
29 Sep 2016 16:29:16,055 DEBUG: at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
29 Sep 2016 16:29:16,095 DEBUG: at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
29 Sep 2016 16:29:16,186 DEBUG: ##### ERROR ------------------------------------------------------------------------------------------
29 Sep 2016 16:29:16,242 DEBUG: ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-gf185a75):
29 Sep 2016 16:29:16,292 DEBUG: ##### ERROR
29 Sep 2016 16:29:16,396 DEBUG: ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
29 Sep 2016 16:29:16,513 DEBUG: ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
29 Sep 2016 16:29:16,556 DEBUG: ##### ERROR Visit our website and forum for extensive documentation and answers to
29 Sep 2016 16:29:16,625 DEBUG: ##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
29 Sep 2016 16:29:16,754 DEBUG: ##### ERROR
29 Sep 2016 16:29:16,848 DEBUG: ##### ERROR MESSAGE: Invalid JEXL expression detected for DP-LT10 with message no message
29 Sep 2016 16:29:16,941 DEBUG: ##### ERROR ------------------------------------------------------------------------------------------
Thanks for any help.