Recently, there have been lots of study for disease-genetic association using SNPs and haplotypes. Statistical methods and tools for various types of data are developed by many researchers. However, there is no unified software which can handle most of major analysis, and the methods and manners to deal with data are quite different through softwares. And thus it is not easy to researcher to choose proper software. In this study, we devide analyzing procedures into three steps: preliminary analysis, population-based analysis and family-based analysis. We review the statistical methods for each step and compare the features of the FBAT, SAS/Genetics, SAGE and R as major integrating softwares for genetic study.