I recently tried to use a GaTK command I previously used with GaTK 3.5, and I'm getting a jexl error.
I don't understand why. I've updated to java 1.8.0_77
java -Xmx${MEM} -jar ${gatk_dir}/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R ${genome} \
-L ${CHROM} \
-V ${data_dir}/'14a_'${abb}'HapCaller_mergedCHRs_VARIANTS'${CHROM}'.vcf' \
-G_filter "DP < 10 " \
-G_filterName "LowCov" \
-G_filter "DP > 100 " \
-G_filterName "HighCov" \
-G_filter "GQ < 20 " \
-G_filterName "LowGQ" \
--clusterWindowSize 10 --clusterSize 3 \
--filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0 " \
--filterName "gatkHardFilter" \
--setFilteredGtToNocall \
-o ${data_dir}/'14b_newgatk_'${abb}'HapCaller_mergedCHRs_VARIANTS_hard_cluster_filterflag_DPGQmissing'${CHROM}'.vcf'
The error message:
ERROR --
ERROR stack trace
java.lang.IllegalArgumentException: Invalid JEXL expression detected for HighCov with message no message
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:136)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:93)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:22)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:323)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:433)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:349)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:97)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)