JEXL and SelectVariants

golharam

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?

Geraldine_VdAuwera

Probably the parentheses, would be my guess. The JEXL syntax is not up to us, and sometimes it's difficult to divine the correct way up front. So trial and error it is. Anyway, glad to hear you got it to work!

golharam

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

Geraldine_VdAuwera

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

Geraldine_VdAuwera

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

golharam

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.