Logistic regression is a common analysis tool used for GWAS when your response variable of interested is qualitative. It comes as one of the standard tools in most GWAS packages (e.g. PLINK).
Most logistic regression models for GWAS would be setup as:
log(odds of disease) = \beta_0 + \beta_1*X
Where X is number of copies of the minor allele for a particular SNP of interest. However, suppose that my case-control data is matched (In my case matched by age, BMI, reported ethnicity, and distance to procurement site). I don't think standard logistic regression (as I have outlined above) is valid. What does everybody do? I don't see options for this in packages like PLINK.