This tutorial is a modification of the tutorial at https://github.com/MareesAT/GWA_tutorial. We modified the commands so that they could be run on Windows computers. If you use Unix-based computers (MacOs and Linux) please use the commands and codes present in the original repository.
The commands for the first step, the Quality Control (QC), will be inside the folder 1_QC_GWAS present on this GitHub. After conclude all steps of QC topic, you can proceed to the next tutorial, the 2_Population_stratification.