When a well-defined phenotype has been selected for a study population, and genotypes are collected using sound techniques, the statistical analysis of genetic data can begin. The de facto analysis of genome-wide association data is a series of single-locus statistic tests, examining each SNP independently for association to the phenotype. The statistical test conducted depends on a variety of factors, but first and foremost, statistical tests are different for quantitative traits versus case/control studies.
