This alternative modeling strategy raises the question of whether, and to what extent, it is advantageous to model the study sample jointly at untyped SNPs. One argument [20] holds that there is no point in jointly modeling such SNPs because all of the linkage disequilibrium information needed to impute them is contained in the reference panel. A counterargument is that, as with any statistical missing data problem, the “correct” inference approach is to create a joint model of all observed and missing data. We have found that a full joint model may indeed improve accuracy on small, contrived imputation datasets (data not shown), and this leads us to believe that joint modeling could theoretically increase accuracy in more realistic datasets.
