Link Search Menu Expand Document

Optional Parameters

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
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
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
regenie_bsize_step1 1000 Size of the genotype blocks
regenie_bsize_step2 400 Size of the genotype blocks
regenie_sample_file empty Sample file corresponding to input BGEN file
regenie_skip_predictions false Skip Regenie Step 1 predictions
regenie_min_imputation_score 0.00 Minimum imputation info score (IMPUTE/MACH R^2)
regenie_min_mac 5 Minimum minor allele count
regenie_range ’ ‘ Apply regenie only on a specify region [format=CHR:MINPOS-MAXPOS]
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
regenie_force_step1 false Run regenie step 1 when >1M genotyped variants are used (not recommended)
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]
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