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Re-use step 1 predictions

If you set save_step1_predictions to true, the pipeline will save the step 1 predictions in regenie_step1_preds folder.

These predictions can be re-used in further analyses on the same dataset when phenotype(s) and covariates are the same. This is useful for example to perform a rare variant analysis on the same dataset used for a previous GWAS analysis.

You can load level 1 preds from this folder in subsequent analyses by setting regenie_premade_predictions to a path like /results/regenie_step1_preds/regenie_step1_out*.

The pipeline then expects the following:

  • A file named regenie_step1_out_pred.list must be present
  • One file per phenotype is expected named regenie_step1_out_1.loco.gz regenie_step1_out_2.loco.gz, ...
  • phenotypes and covariates used in the new analyses must be exactly the same used to generate step1 predictions and column names for phenotypes must be configured in phenotypes_columns in the same order as in the original analysis.