Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

Is it possible to use VariantFiltration to pass (unfilter) variants?

dayzcooldayzcool Member
edited March 2018 in Ask the GATK team

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' \
--filter-name "PASS"

Thank you!

Post edited by dayzcool on

Issue · Github
by Sheila

Issue Number
Last Updated


Sign In or Register to comment.