GWAS
We used regenie for the FinnGen R12 release. Regenie's main advantages are fast leave-one-chromosome-out relatedness calculation which avoids proximal contamination, and use of an approximate Firth test which gives more reliable effect size estimates for rare variants.
Regenie version 2.2.4 was used for the majority of endpoints. Regenie version 3.3 was used for endpoints that did not converge under regenie 2.2.4.
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We analyzed:
2,502 endpoints
2,499 binary endpoints
3 quantitative endpoints (HEIGHT_IRN, WEIGHT_IRN, BMI_IRN)
500,348 samples
282,064 females
218,284 males
21,311,644 variants
We included the following covariates in the model: sex, age, 10 PCs, Finngen chip version 1 or 2 , and legacy genotyping batch.
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