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.
VariantFiltration: how to filter samples where less then 95% of reads agree with the called genotype
I've been looking over the documentation for VariantFilteration and jexl (http://gatkforums.broadinstitute.org/gatk/discussion/1255/using-jexl-to-apply-hard-filters-or-select-variants-based-on-annotation-values) to figure out how to do this, but I can seem to find an answer.
I would like to filter snips where there are many reads that disagree with the called genotype (eg FORMAT 1:20,60:80:99:1900,0).
In pseudo code, I'd like to write something like "AD[GT]/DP<0.95", where the allelic depth (AD) for the called genotype (GT) divided by the total depth (DP) < 0.95. However, the docs indicate that it is not possible to access GT:
"For now, you can filter based on most fields as normal (e.g. GQ < 5.0), but the GT (genotype) field is an exception"
Is there another way to accomplish what I want using VariantFiltration? It seems like a common sense filter, and it's also something I frequently see in the literature for snips in haploid organisms.