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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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Different P-values between REGENIE and PLINK software #445

Open FMinnai opened 1 year ago

FMinnai commented 1 year ago

Hi everyone,

I performed an analysis with REGENIE on 2058 patients with a quantitative trait and 7 different covariates. For 5 SNPs I reached a p-value < 5x10-8.

I repeated the linear regression with PLINK and these 5 SNPs are always the top significant, but with a p-value around 1x10-6.

To perform a check, I used another linear phenotype and I performed the GWASes. P-values from both the two softwares are quite similar (around 1x10-6).

I was wondering the reason of this difference in p-values, if there is any trouble maybe (probably related to the genetic predictors in the Step 1?), and which software I can trust. Thank you for your kind help and suggestions,

Best regards, Francesca

joellembatchou commented 11 months ago

Hi Francesca,

Could you send the logs for the REGENIE and PLINK runs?

Cheers, Joelle