Applying externally generated polygenic risk scores to a VDS


#1

I have a VDS with genetic information in a population, and a set of variant-level scores that I’d like to apply into the people in my VDS. I don’t need any clumping, etc, because that is (in effect) already handled by my external scoring tool (LDPred in this case). I just need to project the scores onto the individuals based on their genotype. Is that type of operation handled in Hail?

Also, this might be something that is handled in the docs – apologies if so – but the docs are currently down!

https://hail.is/hail/sql.html
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#2

Ah, that link is from an old build of the docs. When we moved our system over, some old links broke.

The docs are found at https://www.hail.is/docs/0.2/

Here’s a bit about PRS:
https://hail.is/docs/0.2/guides/genetics.html#polygenic-risk-score-calculation