SAIGE

SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model. It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N > 400,000). SAIGE performs single-variant association tests for binary traits and quantitative traits. For binary traits, SAIGE uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) to account for case-control imbalance. SAIGE-GENE (implemented in the SAIGE R package) performs gene- or region-based association tests (Burde, SKAT, SKAT-O) for binary traits and quantitative traits. Note: SAIGE-GENE accounts for case-control imbalance in gene-based tests (>= 0.35.8.5)