SNPMStat is a command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis
:: MORE INFORMATION
Hu, Y. J., Lin, D. Y. and Zeng, D. (2010),
“A General Framework for Studying Genetic Effects and Gene-Environment Interactions with Missing Data“,
Biostat (2010) 11 (4): 583-598.