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.