SNPTEST stratification analysis

Question

[Cindy]

Hi all,

I used SNPTEST for GWAS analysis stratified by sex, but the results are totally different with and without sex in the cov_names.

SNPTEST said "when using -stratify_on, you should (almost) always specify the same variables to -cov_names to allow for a different baseline between strata. In case-control settings it almost never makes sense to stratify effects but not baseline parameters."

I am not sure how it model the analysis if add sex in the cov_names.

Thanks