I recently performed genome-wide association with phenotypes that were not continuous but fell in categories. I therefore looked for tests that could extend the classical association test for binary phenotypes (like 0/1, resistant/susceptible) to several categories (in my case a combination of binary phenotypes, which could be coded as 0001, 0011, 0111 etc.). While I struggled to compile it on the servers I am using, I have been really satisfied with the results. Note that the software is able to perform fine-mapping and assesses which specific category is associated with SNP variation. It also allows comparing outputs based on frequentist and bayesian approaches. Enjoy !
You can downloadTrinculo for Mac and Linux here : https://sourceforge.net/projects/trinculo/files/?source=navbar