Nominal mapping¤

Nominal mapping reports every variant association within each phenotype's cis window. Use it when downstream analysis needs a complete local summary-statistics table rather than one calibrated lead association per gene.

jaxqtl nominal \
  --bfile tutorial/input/chr22_N100 \
  --pheno tutorial/input/CD4_NC.N100.bed.gz \
  --covar tutorial/input/donor_features.tsv \
  --gene-list tutorial/input/genelist_10 \
  --model nb \
  --test wald \
  --set-offset-from-libsize \
  --normalize-covar \
  --out tutorial/output/nominal

This writes tutorial/output/nominal.nominal.wald.parquet.gz.

The --window value defaults to 500,000 bases. By default, the interval extends from TSS - window through TES + window. Add --tss-centered to instead use TSS - window through TSS + window. Unlike cis, nominal mode does not run Beta-permutation calibration or ACAT.

Score and SPA tests share one null fit per phenotype; GLM Wald tests fit each variant's full model. See Troubleshooting for model controls and Run large scans for performance.

See Nominal output for the output columns.

See the Mapping command reference for all options and defaults.