JEXL and SelectVariants
Posted in Ask the GATK team | Last updated on 2013-03-14 19:37:44


Comments (5)

I'm trying to use JEXL to filter variants but something isn't working and I can't figure it out. I'm hoping someone can point me in the right direction. My VCF file contains an INFO field 1000g2012Apr_ALL. Some of the variants in my VCF have an entry for this field, some don't. I want to filter my VCF file for entries that are below a certain value or are NULL (empty).

Here's what my command looks like:

java -Xmx4G -jar GenomeAnalysisTK.jar -T SelectVariants -R hg19.fa -V my.vcf -o my.1kgfiltered.vcf -select 'vc.getAttribute("1000g2012Apr_ALL") < 0.01' -select '!vc.hasAttribute("1000g2012Apr_ALL")'

The problem is the 2nd select statement. I can't seem to get a JEXL select statement to give me the entries where 1000g2012Apr_ALL are empty. How do I accomplish this?


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