Skip to content

Output schemas¤

Mapping outputs are compressed Parquet files. Columns specific to the Negative Binomial model or permutation calibration are omitted when they do not apply.

Cis output¤

jaxqtl cis writes ${out}.cis.${test}.${perm|acat}.parquet.gz.

Group Columns
Phenotype phenotype_id, chrom, num_var
Lead variant snp, a1, a0, pos, tss_distance, af, ma_count
Association beta, se, pvalue, pvalue_adj, adj_method
Model nb_alpha, negloglikelihood, model_converged
Validity result_valid, failure_reason
Beta calibration shape1, shape2, nc_estimate, perm_converged

The Beta-calibration fields are not emitted for ACAT. nb_alpha is not emitted for Gaussian or Poisson models. negloglikelihood is the fitted negative log-likelihood objective (lower is better). Score and SPA tests report the shared null-model objective; Wald tests report the selected variant's full-model objective.

Invalid rows preserve the tested phenotype

A gene with no finite SNP-level p-values remains in the cis output with result_valid = false. Its lead variant, association statistics, and convergence values are null. Use failure_reason to distinguish this state from a valid association with a large p-value.

Nominal output¤

jaxqtl nominal writes ${out}.nominal.${test}.parquet.gz with one row per phenotype–variant pair:

  • phenotype_id, chrom, snp, pos, a1, a0, tss_distance, af, ma_count.
  • beta, se, pvalue, negloglikelihood, model_converged.
  • nb_alpha for Negative Binomial models.

For score and SPA tests, negloglikelihood is shared across all variants for a phenotype because they use one fitted null model. For Wald tests, it is the fitted full-model objective for that phenotype–variant pair.

Trans output¤

jaxqtl trans writes two files:

  • ${out}.trans.${test}.variant.info.parquet.gz contains chrom, snp, pos, a1, a0, af, and ma_count.
  • ${out}.trans.${test}.sumstats.parquet.gz contains phenotype, snp, beta, se, pvalue, model_converged, and nb_alpha for Negative Binomial models.

Within each phenotype block, summary-statistics rows follow the variant order in the metadata file.