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 |