HERE we are maintaining an newly improved stable version of SAIGE and SAIGE-GENE+. Please find the https://saigegit.github.io/SAIGE-doc/ for documentation.

SAIGE is an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks. The method

• accounts for sample relatedness based on the generalized mixed models
• allows for model fitting with either full or sparse genetic relationship matrix (GRM)
• works for quantitative and binary traits
• handles case-control imbalance of binary traits
• computationally efficient for large data sets
• performs single-variant association tests
• provides effect size estimation through Firth's Bias-Reduced Logistic Regression
• performs conditional association analysis

SAIGE-GENE (now known as SAIGE-GENE+) are new method extension in the R package for testing rare variant in set-based tests.

• performs BURDEN, SKAT, and SKAT-O tests
• allows for tests on multiple minor allele frequencies cutoffs and functional annotations
• allows for specifying weights for markers in the set-based tests
• performs conditional analysis to identify associations independent from nearly GWAS signals

The package takes genotype file input in the following formats

• PLINK (bed, bim, fam), PGEN, BGEN, VCF, BCF, SAV