PCA Adjustment

To account for potential confounding effect due to population stratification, we extract principal components from the genetic data using flashpca. We follow the recommended procedure for this tool which implies some preprocessing and filtering.

In principle, you shouldn't need to change these parameters apart from the number of principal components (NB_PCS).

• NB_PCS (optional, default: 6): The number of PCA components to extract.
• LD_BLOCKS (optional): A path to pre-identified linkage disequilibrium blocks around the variants that will be queried for causal effect estimation. Those LD blocks will be removed from the data used for PCA.
• FLASHPCA_EXCLUSION_REGIONS (required, default: assets/exclusionregionshg19.txt): A path to the flashpca special exclusion regions which is provided in their repository.
• MAF_THRESHOLD (optional, default: 0.01): Only variants with that minor allele frequency are used to compute principal components.