search

jrs95 / hyprcoloc

Hypothesis Prioritisation in multi-trait Colocalization
https://jrs95.github.io/hyprcoloc/
GNU General Public License v3.0
46 stars 12 forks source link

Do GWAS summary statistics have to be independent / come from different samples? #12

Closed MalteThodberg closed 4 years ago

MalteThodberg commented 4 years ago

I'm analyzing a GWAS study where association has been calculated using the same samples across hundreds of phenotypes. So the GWAS summary statistics are not independent.

Is it still appropriate to run hyprcoloc in this case?

jrs95 commented 4 years ago

Hi,

Yes, it is still appropriate to run hyprcoloc on GWAS analyses that are not independent. Although we have an option to account for the correlation, we recommend that you use the standard model (as if the GWAS were independent) as this is much faster and performed well in simulations compared to the correlated model.

Best wishes,

James

MalteThodberg commented 4 years ago

Thanks, I will give hyprcoloc a spin then!