Command-line interface¤
The jaxqtl executable provides four subcommands:
| Command | Result |
|---|---|
jaxqtl compute-pcs |
Expression principal components appended to covariates |
jaxqtl cis |
One lead association and adjusted p-value per tested phenotype |
jaxqtl nominal |
Every association within each cis window |
jaxqtl trans |
Chunked phenotype-by-variant associations |
Run jaxqtl COMMAND --help for the complete parser-generated option list and defaults.
Common mapping options¤
All mapping commands require one genotype source plus --pheno and --covar.
| Group | Options |
|---|---|
| Genotypes | --bfile, --pfile, --vcf, --bgen, --dosage |
| Covariates | --covar-name, --rm-covar, --normalize-covar, --one-hot, --no-intercept |
| Library-size adjustment (offsets) | --offset, --offset-name-from-covar, --set-offset-from-libsize |
| Model and variant testing | --model, --test, --robust-se, --spa |
| Gene-level testing | --acat, --nperm |
| Filters | --keep, --exclude, --min-indiv-expr-pct, --min-gene-expr-pct, --maf, --chr |
| Phenotypes | --gene-list, --genes, --window, --tss-centered |
| Solver | --max-iter, --tol, --gtol, --step-size, --solver |
| Runtime | --seed, --platform, --verbose, --out |
Some accepted flags apply only to particular combinations. --robust-se requires a Wald test; --spa applies to
score tests; --acat and --nperm affect only cis; and --window and --tss-centered affect only cis and
nominal.
For score-test ACAT scans, --spa --acat is strongly recommended because ACAT is sensitive to variant
p-value calibration. See Tests and gene-level calibration
for why Beta permutation does not have the same dependence on asymptotic tail probabilities.
Mapping automatically retains expression phenotypes on chromosome labels shared with the genotype input. --chr
further restricts both phenotypes and genotype variants to one exact label, which must occur in both inputs.
See the workflow guides for complete commands with compatible options.
GLM fitting controls¤
| Option | Default | Meaning |
|---|---|---|
--max-iter |
1000 |
Maximum IRLS iterations |
--tol |
1e-3 |
Absolute change in total negative log likelihood that triggers the gradient check |
--gtol |
1e-3 |
Per-observation gradient tolerance, with coefficient scaling and NB2 bound projection |
--step-size |
1.0 |
Initial trial step for each IRLS update; rejected trials are halved |
--solver |
cholesky |
Weighted least-squares solver; choices are cholesky, qr, and cg |
Both likelihood and gradient criteria must be met for GLM convergence. These controls govern model fitting; they do not set the SPA root-solver or Beta-calibration tolerances. See Troubleshooting for interpretation and troubleshooting.