GWAS
We used the SAIGE software for running R6 GWAS as we did in previous releases. SAIGE is a mixed model logistic regression R/C++ package. We used code of version 0.39.1: https://github.com/weizhouUMICH/SAIGE/tree/finngen_r6_jk We made two modifications to SAIGE 0.39.1 codebase (neither modification affects the method):
Null model .rda objects are trimmed to reduce RAM consumption
Ref hom, het, and alt hom counts in cases and controls are included in the output, summing the probabilities of each genotype over individuals, different from the 0.39.1 implementation in SAIGE in which the counts are sums of most probable genotypes over individuals
We analyzed:
2,861 endpoints
260,405 samples
16,962,023 variants
We included the following covariates in the model: sex, age, 10 PCs, genotyping batch.
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