assoc

Perform genome-wide association study (GWAS) using mixed linear models.

Use this command with GRM input from grm.

Basic Syntax

Minimum Working Command
gelex assoc -b genotypes -p phenotypes.tsv --grm my_grm -o gwas_run
Full Syntax Template
gelex assoc --pheno <pheno_file> --bfile <genotype_prefix> --grm <grm_prefix...> [OPTIONS]

Required inputs are phenotype file (--pheno), genotype prefix (--bfile), and at least one GRM prefix (--grm).

Method Selection

Pick model and preprocessing strategy before tuning runtime options.

Warning

If you use --transform with --model d, dominance signals may be attenuated, which can reduce power to detect dominance effects.

Options

Quick Start Options

-p, --pheno required

Phenotype TSV file in format FID IID trait1 ....

-b, --bfile required

PLINK binary prefix (.bed/.bim/.fam).

--grm required

One or more GRM prefixes.

-o, --out gelex

Output prefix for GWAS results.

Input and Covariate Options

--pheno-col 2

0-based trait column index in phenotype file.

--qcovar

Quantitative covariate TSV in format FID IID covar1 ....

--dcovar

Categorical covariate TSV in format FID IID factor1 ....

Model Configuration

--model a

Association model: a (additive) or d (dominance).

--geno-method OrthCenterHWE

Genotype processing method. Available methods: StandardizeHWE (SH), CenterHWE (CH), OrthStandardizeHWE (OSH), OrthCenterHWE (OCH), Standardize (S), Center (C), OrthStandardize (OS), OrthCenter (OC). Abbreviations accepted. See Genotype Processing Methods.

--transform none

Phenotype transform: none, dint (Direct INT), iint (Indirect INT).

--int-offset 0.375

INT offset parameter k.

REML and Performance

--max-iter 100

Maximum REML iterations.

--tol 1e-06

REML convergence tolerance.

-c, --chunk-size 10000

Number of SNPs per association-testing chunk.

-t, --threads half of available CPU cores

Number of CPU threads to use.

--loco false

Enable leave-one-chromosome-out analysis.

Output Files

After a successful run, GWAS summary statistics are written to:

File pattern

Contents

Reference

<out>.gwas.tsv

SNP-wise test statistics (effect size, SE, P-value, allele fields)

GWAS Results (.gwas.tsv)

Warnings and Notes

Warning

--loco requires chromosome-wise GRM inputs generated from gelex grm --loco. Use the matching GRM prefix in --grm.

Note

For --model d, provide GRM inputs consistent with the dominance model setup (typically additive + dominance GRMs).

Examples

Standard Additive GWAS
gelex assoc \
   -b genotypes_qc \
   -p phenotypes.tsv \
   --grm my_grm \
   -o basic_gwas
Add Quantitative and Categorical Covariates
gelex assoc \
   -b genotypes_qc \
   -p phenotypes.tsv \
   --grm my_grm \
   --qcovar pcs.tsv \
   --dcovar sex.tsv \
   -o covar_gwas
LOCO Analysis
gelex assoc \
   -b genotypes_qc \
   -p phenotypes.tsv \
   --grm my_grm.add \
   --loco \
   -o loco_gwas
Dominance Model with Two GRMs
gelex assoc \
   -b genotypes_qc \
   -p phenotypes.tsv \
   --grm my_grm.add my_grm.dom \
   --model d \
   --transform iint \
   -o dom_gwas
Larger Thread Count
gelex assoc \
   -b genotypes_qc \
   -p phenotypes.tsv \
   --grm my_grm \
   --threads 16 \
   -o fast_gwas

See Also