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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' \