GWAS
We used regenie for release 8. 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.
We used regenie version 2.2.4.
Links:
The Docker image used in the analysis is available in Docker Hub.
We analyzed:
2,202 endpoints
342,499 samples
20,175,455 variants
We included the following covariates in the model: sex, age, 10 PCs, genotyping batch.
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