There are 2 comments on this article. To see them or add your own, view this post on the forum

Hello,

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:

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Invalid command line: Invalid JEXL expression detected for synon with message For input string: "nan"

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?

Thanks!

There are 2 comments on this article. To see them or add your own, view this post on the forum