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broadinstitute / seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
22 stars 20 forks source link

adding pext scores as an in silico score in seqr #236

Open hanars opened 3 years ago

hanars commented 3 years ago

@anneodonnell commented on Wed Jun 26 2019

pext scores are Beryl's transcript aware expression score. I was hoping it could be added to the in silico list. We use it in the opposite way from most scores - we use the score to downweight variants but it can't really upweight a variant - as it identifies variants that are in regions of a gene that don't appear to be expressed.

Recommended color scheme 0-0.2 color, 0.21-1 gray we want the color to catch people's attention but not be red, yellow or green. What would you think about having these be purple (or whatever color that could catch attention without screaming look at me).

I'm not totally sure where the pext score data lives but it's in the gnomAD browser. Either Beryl, Nick or Matt should be able to help.

mike-w-wilson commented 2 years ago

We do not have pext scores for 38 so this will only be implemented in 37

mike-w-wilson commented 2 years ago

Waiting til gnomAD updates gencode