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I'm currently running variantEval to count up variants per individual stratified by a variety of annotations.
My GATK call looks like:
java -jar /humgen/gsa-hpprojects/GATK/bin/current/GenomeAnalysisTK.jar \
-T VariantEval \
-R Homo_sapiens_assembly19.fasta \
-o output.txt \
-L input.vcf \
-eval input.vcf \
-ST Sample -noST \
-noEV -EV CountVariants \
-ST JexlExpression --select_names "nonsynon" --select_exps "resource.VAT_CDS == 'nonsynonymous' && resource.FOUNDERS_FRQ > 0.05" \
-ST JexlExpression --select_names "synon" --select_exps "resource.VAT_CDS == 'synonymous' && resource.FOUNDERS_FRQ > 0.05" ...
where the VAT_CDS section of the INFO field in the VCF has a functional annotation or is set to "na" if an annotation is unavailable. I'm getting the following error:
but weirdly the error is not consistent (my data is stratified by chromosome and most chromosomes will run without throwing the error while one or two chromosomes do exhibit the error. Do you have any ideas what's causing this behavior?