From UABgrid Documentation
Impute is a program for estimating ("imputing") unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST.
Steps to run Impute
Impute 2.0.3 has been installed on Cheaha. Once you login to Cheaha, set up your environment with the following
module load impute/impute