broadinstitute / genetic-prevalence-estimator

https://genie.broadinstitute.org/
BSD 3-Clause "New" or "Revised" License
1 stars 0 forks source link

Add option to include gnomAD missense with REVEL score >.932 #146

Closed sambaxter closed 6 months ago

sambaxter commented 1 year ago

We would like to also add the option for users to include gnomAD missense with REVEL score >.932 when they use the "Recommended feature". This option should appear at the bottom of the page above the submit button.

Text to add: Include gnomAD variants based on variant type? High Confidence Loss of Function only High Confidence Loss of Function and Missense Variants withStrong REVEL score (>.932)

image
sambaxter commented 6 months ago

@rileyhgrant - it was pointed out to me that I made a mistake when I wrote the requirements to this as >0.932. It is actually greater than or equal to .932

Can you update the requirements to also include variants with the REVEL score .932? It will also need to update the website text to be "High Confidence Loss of Function and Missense Variants with Strong REVEL score (≥.932)"

rileyhgrant commented 6 months ago

Oops, I think this was on me too, I think verbally I got the >= 0.932, as that is currently what the logic does when filtering:

include_from_gnomad = (
            PLOF_VEP_CONSEQUENCE_TERMS.contains(ds.major_consequence) & (ds.lof == "HC")
        ) | ((ds.major_consequence == "missense_variant") & (ds.revel_score >= 9.32e-1))

notably: ds.revel_score >= 9.32e-1

So that's just to say we're good on the actual filtering going on, I'll fix the text to correctly say greater than or equal to.


Edit: resolved by #194