esalvi · ✭

Using GATK 3.6 with Variant Filtration I obtained an error applying --genotypeFilterName. My current pipeline of commands is as follows: java -jarGenomeAnalysisTK.jar -T VariantFiltration -R hg19.fa -V myfile.vcf --genotypeFilterExpression 'GQ < 50.0' --genotypeFilterName 'lowGQ' --genotypeFilterExpression 'DP < 10.0' --genotypeFilterName 'lowDP' -o myfile.postCGP.Gfiltered.vcf ERROR MESSAGE: Invalid JEXL expression detected for lowDP with message no message for low GQ it runs. in my vcf (created with HaplotypeCaller GVCF and GenotypeGVCF) I have the field DP at genotype INFO FORMAT= INFO= What's the problem? thanks

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