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JEXL and SelectVariants

golharamgolharam Posts: 28Member ✭✭
edited March 2013 in Ask the GATK team

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?

Best Answer


  • golharamgolharam Posts: 28Member ✭✭

    -select '(!vc.hasAttribute("1000g2012Apr_ALL")) || vc.getAttribute("1000g2012Apr_ALL") < 0.01'

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,565Administrator, Dev admin

    Not sure about the proper syntax, but have you tried something like -select '!(vc.hasAttribute("1000g2012Apr_ALL"))' or -select '! vc.hasAttribute("1000g2012Apr_ALL")'?

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,565Administrator, Dev admin

    Oh, well there you go, ignore my feeble attempt! (I hate JEXL)

    Geraldine Van der Auwera, PhD

  • golharamgolharam Posts: 28Member ✭✭

    Its odd that I had to combine the two select statements to get it to work. Or perhaps maybe it was the addition of the parentheses.

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