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A flow chart of the two-step piecemeal imputation framework, including both the training phase through a 5-fold cross validation and the independent testing. In the chart, T is the set of markers in the lower density chip and T∪U is the set of markers in the higher density chip; m i is a marker of U; S is the set of study samples genotyped on T and R is the set of references genotyped on T∪U. The goal is to impute the genotype for markers of U for the study samples
