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Optional Parameters

General

Option Default Description
outdir “output/${params.project}” Output directory
project_date today Date in report
covariates_filename empty path to covariates file
covariates_columns empty List of covariates
phenotypes_delete_missings false Removing samples with missing data at any of the phenotypes

Pruning Step

Option Default Description
prune_enabled false Enable pruning step
prune_maf 0.01 MAF filter
prune_window_kbsize 1000 Window size
prune_step_size 100 Step size (variant ct)
prune_r2_threshold 0.9 Unphased hardcall R2 threshold

Quality Control (QC) of Predictions

Option Default Description
qc_maf 0.01 Minor allele frequency (MAF) filter
qc_mac 100 Minor allele count (MAC) filter
qc_geno 0.1 Genotype missingess
qc_hwe 1e-15 Hardy-Weinberg equilibrium (HWE) filter
qc_mind 0.1 Sample missigness
Option Default Description
vcf_conversion_split_id false If false, family and individual IDs are set to the sample ID (using plink2 --double-id option). If true, split VCF by “_” into FID and IID (--id-delim)

Prediction Step (Regenie Step 1)

The following parameters are all regenie specific. Please click here to learn more about them.

Option Default Description
regenie_skip_predictions false Skip Regenie Step 1 predictions
regenie_force_step1 false Run regenie step 1 when >1M genotyped variants are used (not recommended)
regenie_bsize_step1 1000 Size of the genotype blocks

Single-variant and Gene-based Tests (Regenie Step 2)

The following parameters are all regenie specific. Please click here to learn more about them.

Option Default Description
regenie_bsize_step2 400 Size of the genotype blocks
regenie_firth true Use Firth likelihood ratio test (LRT) as fallback for p-values less than threshold
regenie_firth_approx true Use approximate Firth LRT for computational speedup

Single-variant Tests Only

Option Default Description
regenie_sample_file empty Sample file corresponding to input BGEN file
regenie_min_imputation_score 0.00 Minimum imputation info score (IMPUTE/MACH R^2)
regenie_min_mac 5 Minimum minor allele count
regenie_ref_first false Specify to use the first allele as the reference allele for BGEN or PLINK bed/bim/fam file input [default is to use the last allele as the reference]

Gene-based Tests Only

The following gene-based parameters are all regenie specific. Please click here to learn more about them.

Option Default Description
regenie_gene_aaf 1 % comma-separated list of AAF upper bounds to use when building masks
regenie_gene_test - comma-separated list of SKAT/ACAT-type tests to run
regenie_gene_joint - comma-separated list of joint tests to apply on the generated burden masks
regenie_gene_build_mask max build masks using the maximum number of ALT alleles across sites, or the sum of ALT alleles (‘sum’), or thresholding the sum to 2 (‘comphet’)
regenie_write_bed_masks - write mask to PLINK bed format (does not work when building masks with ‘sum’)
regenie_gene_vc_mac_thr 10 MAC threshold below which to collapse variants in SKAT/ACAT-type tests
regenie_gene_vc_max_aaf 100% AAF upper bound to use for SKAT/ACAT-type tests

R Report

Option Default Description
annotation_min_log10p 5 Filter and annotate results with logp10 >= 5
plot_ylimit 0 Limit y axis in Manhattan/QQ plot for large p-values
manhattan_annotation_enabled true Use annotation for Manhattan plot