Comparision of the efficacy of three SNPs data simulation methods
Objective To compare the differences in the efficacy of HAPGEN2,gs2.0 and GWAsimulator2 in simulating single nucleotide polymorphisms (SNPs) data,and to provide guidance for the future use of SNPs data simulation methods.Methods The simulation data were generated by the above-mentioned three methods using the real population SNPs data as the original data.The simulation performance was evaluated by the linkage disequilibrium model and the minimum allele frequency,and the setting efficiency of the disease site was evaluated by x2 difference.Results The ability of HAPGEN2 to simulate the linkage disequilibrium model was superior to those of gs2.0 and GWAsimulator2.The abilities of gs2.0 and GWAsimulator2 to simulate the minimum allele frequency were similar to as well as superior to that of HAPGEN2,and all the three methods could be used to set the single disease site.Conclusions The three SNPs data simulation methods have advantages and disadvantages,and the users can choose the appropriate simulation method according to the actual demand.
single nucleotide polymorphismscomputer simulationlinkage disequilibriumminimum allele frequency