Linear mixed effect model with plink bfile dataset

Question

[ruyu.s]

I have a WGS result (in plink bfile format) and a longitudinal phenotype of interests. I am confused about how to fit the WGS data and the phenotype of interest into the linear mixed model. I also found some publications using GWAS data to do the mixed linear model, but after I read through these, I still feel confused. Please Help me!