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
association_build (deprecated: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 this feature.

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

Interaction Tests

Starting from regenie v3.0, you can perform scans for interactions (either GxE or GxG). Please click here to learn more about this feature.

Option	Value	Description
regenie_run_interaction_tests	true (default: false)	Activate interaction testing
regenie_interaction	null	to run GxE test specifying the interacting covariate
regenie_interaction_snp	null	to run GxG test specifying the interacting variant

Conditional analyses

Starting from regenie v3.0, you can specify genetic variants to add to the set of covariates when performing association testing. Please click here to learn more about this feature.

Option	Value	Description
` regenie_condition_list`	null	file with list of variants to condition on