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.
Is it possible to use VariantFiltration to pass (unfilter) variants?
I would like to make filtered variants meeting certain criteria PASS. Is it possible to use VariantFiltration? I wonder if GATK provides a tool for this type of task.
For instance, I want to convert PON-filtered variants called by Mutect2 into PASS variants based on their quality. I tried something hacky like this. It's close enough but I would like to know if there is a good way to do this.
$GATK VariantFiltration \
-filter 'panel_of_normals && TLOD > 50.0 && N_ART_LOD < 10.0 && vc.getFilters().size() == 1' \