HAP-SAMPLE is an application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be “genotyped,” along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans.
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Wright, F.A, Huang, H., Guan, X., Gamiel, K, Jeffries, C., Barry, W.T., de Villena, F.P., Sullivan, P.F., Wilhelmsen, K.C., and Zou. F. (2007)
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans,
Bioinformatics 23: 2581-2588.