trios.ped is a linkage file with missing data. (colomns are : family, individual, father, mother, sex, phenotype, SNP1_1, SNP1_2, ...) Use MI-TDT to generate 10 imputed files trios.ped.01 to trios.ped.10: MI-TDT trios.ped Then you can analyse these files separately. An example of analysis with p-value recombination is given in the R script p-values.R