I have just started learning GWAS as I will have to run some of them in the near future and I am pretty confused about which are the best computational tools available for my dataset. In particular, I have almost 10 millions SNPs that I would like to test against clinical numerical covariates such as blood pressure. Moreover, I have some high-dimensional phenotypes that I would like to reduce to 40/50 variables using PCA or ICA and test them in the same multivariate model.
I have been advised to use the R package matrix EQTL for univariate (linear regression) models and from their paper the GEMMA software (http://www.xzlab.org/software.html) looks promising for multivariate ones. However, I would like to year your thoughts about this before starting, please.