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lifebit-ai / gwas

GWAS pipeline using SAIGE
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ToDo: Investigate if the stats for this population can be custom #66

Open cgpu opened 4 years ago

cgpu commented 4 years ago

ToDo: Investigate if the stats for this population can be custom

I see files that indicate we are using sth like a reference population for performing the ldsc analysis. Can this be customised based on the user's population of preference?

Originally posted by @cgpu in https://github.com/lifebit-ai/gel-gwas/pull/57#r509044108

mcamarad commented 4 years ago

Ideally yes, but they should be provided in the exact same format than the original ones. This mean that there's the possibility of using any population to compute genetic correlation and heritability.

Thanks to your refactoring, now it's possible :tada: https://github.com/lifebit-ai/gel-gwas/blob/e3431eba05a4150286b9ed6eff994e5b08fce9de/main.nf#L24-L25