There is a great interest in finding associations between genes and common disease by understanding complex genetic architecture of natural populations. A plethora of methodologies and corresponding software tools has been developed to address this problem. Simulation study is important in evaluating novel methods, testing hypotheses when input data is not easily obtainable or meets specific assumptions. We present cophesim, software to add a phenotype to genotype data prepared by different genetic simulators. The output information of cophesim can be directly usable as an input for different GWAS tools. Usability of cophesim was proven with comprehensive simulation studies.