undefined variable MappingQualityRankSum
I am using GATK version-3.2-2 and called the variants using HaplotypeCaller using the below shown command:
java -jar GenomeAnalysisTK.jar -R ref.fa -T HaplotypeCaller -I input.vcf -L region.bed -stand_emit_conf 10 -stand_call_conf 30 --genotyping_mode DISCOVERY -o var.vcf
And then selected the variants using SelectVariants and filtered using VariantFiltration by following the steps in the tutorial:
https://www.broadinstitute.org/gatk/guide/topic?name=tutorials . However, i met with the following error:
"undefined variable ReadPosRankSum" and undefined variable "MappingQualityRankSum" . The same issue is discussed in the forum but could find a concrete solution to fix this. Could someone help?