Multivariate Permutations Analysis

Question

[Tark]

Hi everyone, i have 12 phenotypes that i want to permute to do multivariate analysis. i tried to generate permutations using plink --make-perm-pheno function. i got 12 files with permuted values. i want to use these permuted data in multivariate association analysis. i am confused how can i do that ?

Any help will be highly appreciated