jiabowang/GAPIT

Different Models showing similar results

Waleedkhan1122 opened this issue · 2 comments

Waleedkhan1122 commented

Hi GAPIT team,

I am using different models to obtain my GWAS results. I am facing an issue, the results of my most of the models are similar. Some models show completely same results such as FarmCPU and GLM. Please guide me what possibly I am doing wrong and how to resolve the issue. Thanks

jiabowang commented

Hi，
The FarmCPU is a multiple-step GWAS model, its first step is based on the GLM. If there are significant markers, they would be put into the next step as covariances.
So if there are no significant markers in the GLM, the final results of GLM and FarmCPU would be the same as each other.

Waleedkhan1122 commented