Use JAMP for multivariate GWAS analysis, based on raw genotypic data.
JAMP uses raw data as input and evaluates the multivariate evidence for association of multiple phenotypes for a SNP. It also provides a family-wise corrected P-value.
For questions e-mail Danielle Posthuma.
Besides JAMP you need to have PLINK from Shaun Purcell installed, which can be downloaded freely from here. In addition, python v2.6 or higher is required and if not already installed can be downloaded from here.