adding pext scores as an in silico score in seqr

[hanars]

@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]

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

[mike-w-wilson]

Waiting til gnomAD updates gencode

[lynnpais]

Updated in gnomAD.