by MV-SNPTEST and TATES, can be used to obtain insight into underlying biology and facilitates the discrimination between independent and pleiotropic QTL effects. Furthermore, MV-PLINK, MultiPhen, TATES and UV-MA allow analysis of a combination of quantitative and binary (case-control) traits [7], [12], [15]. MV-BIMBAM and UV-MA can be applied to summary data, without access to raw phenotype and genotype data [22]. Also, MV-SNPTEST, MultiPhen, TATES, UV-PCA and UV-MA are able to handle genotype probabilities as obtained by imputation while the other methods are not [12], [15], [20]. Finally, our study showed large differences in run time between the methods.
