We have created some code that perform a GWAS analysis of gene-environnement interactions for imputed SNPs and non-imputed SNPs. Instead of using PLINK to perform the logistic regressions or the generalized linear model, we used the PLINK’s R plug-in function to do it for the non-imputed SNPs. For the imputed SNPs, we completely exceeded PLINK and used R to do the statistical tests. For both imputed and non-imputed SNPs, we used BASH scritping to dispatch the analysis on SGE and then gathers the results after the analysis.
The scritps has been implemented using BASH, Perl and R scritping on a Linux workstation and has been tested on Linux only.