Removing variants based on the FORMAT field
I have been trying to remove the Variants in my Sample with a GQ lower than 20 as part of the Genotype Refinement workflow
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R ref.fa -V Genotype_refinement.vcf -G_filter "GQ < 20.0" -G_filterName lowGQ -o Genotype_refinement_GQ.vcf
This gives me a vcf file with the Filter name lowGQ in the FORMAT field.
Now I do not know how to use SelectVariants to remove these filtered variants. I think my JEXL is wrong
java -jar GenomeAnalysisTK.jar -R ref.fa -T SelectVariants -V Genotype_refinement_GQ.vcf -o Genotype_refinement_GQ_filtered.vcf -xl_se 'lowGQ'
I still get the lowGQ samples when I check the file. Could you help me understand how to remove these?
Also I wanted to preferably do this in a single step but apparently GATK SelectVariants does not recognise G_filter
##### ERROR MESSAGE: Argument with name 'G_filter' isn't defined.