Workflow Parameters

• docker_image (default: olivierlabayle/wdl-gwas:main): The docker image used to run the workflow.
• covariates_file: A CSV file containing the set of covariates and phenotypes. Missing values should be represented by empty fields.
• genotypes: PLINK BED files.
• imputed_genotypes: PLINK PGEN files, split by chromosome.
• groupby (default: []): A set of variables used to stratify individuals for which a GWAS will be run independently. If empty, the full dataset is used.
• covariates (default: ["AGE", "SEX", "AGExAGE", "AGExSEX"]): A set of covariates used to adjust for confounding or increase power in the association testing step. Product of variables can be defined using the _x_ syntax, for example: ["AGE", "SEX", "AGExSEX", "AGExAGE"].
• phenotypes: A set of phenotypes for which a GWAS will be run independently.
• min_cases_controls (default: 10): Minimum number of phenotype cases/controls within a group to proceed to GWAS.
• high_ld_regions: File containing high LD regions to be excluded when performing LD pruning for PCA. The file is stored in assets/exclude_b38.txt and needs to be uploaded to the RAP.
• ip_values (default: "1000 50 0.05"): Values used to create independent genotypes for PCA (see here).
• npcs (default 10): Number of principal components to use to account for population structure.
• approx_pca (default: true): Whether to use an approximation to the PCA algorithm (see here).
• maf (default: 0.01): Minor allele frequency threshold. This is used to filter variants for PCA and for plotting GWAS results. The association testing step is still performed across all variants.
• mac (default: 10): Minor allele count used to filter variants for PCA and entering REGENIE's variants.
• regenie_cv_folds (default: 5): Number of folds for Regenie step 1. Can also be loocv.
• regenie_bsize (default 1000): Regenie block size.

For Regenie's options see the online documentation.