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Required Parameters

Our pipeline supports single-variant and gene-based tests. Depending on the use-case, different parameters must be set.

All Tests

Option Value Description
project my-project-name Name of the project
genotypes_prediction (deprecated: genotypes_array) /path/to/allChrs.{bim,bed,fam} Path to the array genotypes (single merged file in plink format).
genotypes_association (deprecated: genotypes_imputed) /path/to/vcf/*vcf.gz or /path/to/bgen/*bgen Path to imputed genotypes in VCF or BGEN format)
genotypes_association_format (deprecated: genotypes_imputed_format) VCF or BGEN Input file format of imputed genotypes
genotypes_build hg19 or hg38 Imputed genotypes build format
phenotypes_filename /path/to/phenotype.txt Path to phenotype file
phenotypes_columns ‘phenoColumn1,phenoColumn2,phenoColumn3’ List of phenotypes
phenotypes_binary_trait false, true Binary trait?

Single-variant Tests Only

Option Value Description
regenie_test additive, recessive or dominant Define test

Gene-based Tests Only

The parameters regenie_gene_anno, regenie_gene_setlist and regenie_gene_masks are all regenie parameters. Please click here to learn more about them.

Option Value Description
regenie_run_gene_based_tests true (default: false) Activate gene-based testing
regenie_gene_anno /path/to/*.annotation File with variant annotations for each set
regenie_gene_setlist /path/to/*.setlist File listing variant sets
     
regenie_gene_masks /path/to/*.masks File with mask definitions using the annotations defined in regenie_gene_anno