Hands-on session of the AG2PI online workshop series: "A Practical Guide to Genome-wide Association Studies (GWAS)" put together by Zihao Zheng.
The object of this hands-on session is to conduct GWAS with some published softwares, using the maize 282 association panel as examples. The choice of GWAS models here are the gold standard mixed linear model (MLM) covered in the presentation, and fixed and random model circulating probability unification (FarmCPU). Highlighed in figure below (Fig from Cortes et al.)
To get ready for the tutorials, please download the following software/R packages to your local machine