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R4
R4
  • Introduction
  • Data download
  • Data description
  • Data releases
  • How to cite
  • Methods
    • Participating biobanks/cohorts
    • Genotypes
      • Genotype data
      • Genotype imputation
      • SISu reference panel
      • Software used
      • LD estimation
    • Endpoints
    • GWAS
      • Sample QC and PCA
      • Association tests
    • Fine-mapping
    • Contact
    • Github
    • FinnGen
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  1. Methods

GWAS

PreviousEndpointsNextSample QC and PCA

Last updated 4 years ago

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We used the SAIGE (version 0.35.8.8) software for running the R4 GWAS.

SAIGE is a mixed model logistic regression R/C++ package, able to account for related samples.

We analyzed:

  • ​2,444 endpoints

  • 176,899 samples

  • 16,962,023 variants

We included the following covariates in the model: sex, age, 10 PCs, genotyping batch.