Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?