Program for frequentist and Bayesian tests of single-nucleotide polymorphism (SNP) association with binary (case-control) and quantitative phenotypes taking genotype uncertainty into account.
The software is part of the Oxford genome-wide analysis software suite (OGWASS).
SNPTEST 2 is a program for the analysis of single SNP association in genome-wide studies.
The tests implemented include:
binary (case-control) phenotypes, single and multiple quantitative phenotypes
Bayesian and frequentist tests
ability to condition upon an arbitrary set of covariates and/or SNPs
various different methods for the dealing with imputed SNPs
The program is designed to work seamlessly with the output of our genotype imputation software IMPUTE 4 and the programs QCTOOL and GTOOL.
Commercial licence is available as part or whole of our software suite, OGWASS.