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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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surface gnomad filter threshold to somatic and immuno workflows #113

Closed malachig closed 1 year ago

malachig commented 1 year ago

This is related to https://github.com/wustl-oncology/analysis-wdls/issues/112

evelyn-schmidt commented 1 year ago

My test succeeded. We set the gnomad threshold to 1.1 so that there is no filtering on gnomad data resulting in the final number of variants called to increase from 126 to 149. This is as expected.

malachig commented 1 year ago

To be clear, we do NOT recommend turning off this filter by setting the value > 1. We want the ability to do this in certain edge cases and for experimentation but recommend the current status quo for now (i.e. filtering out variants that appear in gnomad at >0.1% global AF).