CARAT is a C/C++ program that performs genome-wide association analysis of a binary trait in samples with unknown population structure, adjusting for covariates. The main reference for this program is

Jiang D., Zhong S., McPeek M. S. (2016). Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease. The American Journal of Human Genetics 98, 243-255

CARAT Documentation

Changelog

Download the software (gzipped tar file)