Supported Command-line Options

Input/Output File Options

Option	Description
--bfile	PLINK binary file prefix for each cohort .bim .bed .fam
--ld	PLINK LD file prefix for each cohort .bim .ld (.frq)
--cojo-file	GWAS summary statistics file for each cohort in GCTA-COJO format (Header SNP A1 A2 freq b se p N)
--out	Output file path prefix

Original GCTA Options

These options and flags are functionally identical to those in the original GCTA COJO.

Program mode	Type	Description (exactly one of these three is required)
--cojo-slct	flag	Stepwise iterative selection of independently associated SNPs
--cojo-joint	flag	Calculate joint effects for provided SNPs and exit
--cojo-cond	option	Calculate conditional effects for provided SNPs and exit Must provide a file with a list of SNPs

Option	Description	Default
--cojo-wind	SNP position window in Kb (-1 disables windowing)	10000 (±1e7)
--cojo-p	Significance threshold for SNP selection (0-1)	5e-8
--cojo-collinear	Collinearity threshold for SNP inclusion (0–0.9999)	0.9
--cojo-top-SNPs	Only select a fixed number of independently associated SNPs	10000
--extract	File path of SNPs to be included
--exclude	File path of SNPs to be excluded
--extract-snp	A list of SNPs to be included
--exclude-snp	A list of SNPs to be excluded
--chr	Only include SNPs on a specific chromosome (1-22)
--thread-num	Number of threads to use	1

Below options are extended to multiple cohorts (please see Advanced Usages for example).

Option	Description	Default
--keep	File path of individuals to be included
--remove	File path of individuals to be excluded
--diff-freq	Frequency diff threshold between sumstat and genotype (0-1)	0.2
--maf	Minor allele frequency threshold for genotype (0-0.5)	0
--maf-sumstat	Minor allele frequency threshold for sumstat files (0-0.5)	0
--geno	Missingness threshold in .bed files (0-1)	1 (none)

Manc-COJO Specific Options/Flags

Option	Description	Default
--fix	File path of fixed SNPs for iterative selection
--fix-snp	A list of fixed SNPs for iterative selection
--fix-p	Significance threshold for fixed SNPs (0-1)	5e-8
--fix-col	Collinearity threshold for fixed SNPs (0–0.9999)	0.9
--fix-cojo-col	Collinearity threshold between fixed SNPs and selected SNPs (0–0.9999)	0.9
--R2	R² incremental threshold for forward selection	-1 (none)
--R2back	R² incremental threshold for backward selection	-1 (none)

Flag	Description
--fix-drop	Drop fixed SNPs above --fix-p threshold before SNP selection
--var-from-ld	Estimate genotypic variance from LD reference instead of 2pq
--hetero-report	Output Cochran’s Q heterogeneity statistics (multi-cohort only)
--output-all	Save all .cma.cojo .jma.cojo .ldr.cojo .badsnps files

Algorithm options

Manc-COJO implements three algorithms for both stepwise SNP selection (--slct-mode) and effect size estimation (--effect-mode). Available options include

• GCTA (default, original GCTA behaviour)
  Impute missing genotypes when computing pairwise LD, and additionally adjust for missingness in GWAS summary statistics
• imputeNA
  Only impute missing genotypes when computing pairwise LD
• removeNA
  Only exclude individuals with missing genotypes on a per–SNP-pair basis

Please refer to our paper for detailed methodological descriptions.

Option	Allowed Values	Default	Description
--slct-mode	GCTA, imputeNA, removeNA	GCTA	Iterative SNP selection method
--effect-mode	GCTA, imputeNA, removeNA	GCTA	Effect size estimation method