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surface gnomad filter threshold to somatic and immuno workflows #113

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merged 1 commit into from
Jul 10, 2023

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malachig
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This is related to
#112

@malachig malachig requested a review from tmooney April 21, 2023 16:24
@malachig malachig added the enhancement New feature or request label Apr 21, 2023
@evelyn-schmidt
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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
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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).

@evelyn-schmidt evelyn-schmidt merged commit 3b0cf93 into main Jul 10, 2023
@malachig malachig deleted the gnomad_cutoff branch July 10, 2023 20:36
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