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Required Parameters

Option Value Description
project my-project-name Name of the project
genotypes_array /path/to/allChrs.{bim,bed,fam} Path to the array genotypes (single merged file in plink format).
genotypes_imputed /path/to/vcf/*vcf.gz or /path/to/bgen/*bgen Path to imputed genotypes in VCF or BGEN format)
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?
regenie_test additive, recessive or dominant Define test