SNPTEST is a tool to analyze a single SNP association in genome-wide association studies (GWAS). The SNPTEST algorithm includes functions for case-control phenotypes, single and multiple quantitative phenotypes Bayesian, Frequentist tests, condition using an arbitrary set of covariates and/or SNPs, and several methods for imputed SNPs.
GWAS study
Marchini J, Howie B "Genotype imputation for genome-wide association studies." Nat Rev Genet. 2010 Jul;11(7):499-511. https://doi.org/10.1038/nrg2796
PMID: 20517342
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