Trans mapping¤

Trans mapping tests genotype blocks against every retained phenotype. jaxQTL streams blocks from the genotype source so the entire variant matrix does not need to reside in memory.

jaxqtl trans \
  --bfile tutorial/input/chr22_N100 \
  --pheno tutorial/input/CD4_NC.N100.bed.gz \
  --covar tutorial/input/donor_features.tsv \
  --model nb \
  --test score \
  --set-offset-from-libsize \
  --out tutorial/output/trans

The current CLI reads 2,500 variants per block. It writes variant metadata separately from the phenotype-by-variant summary statistics so metadata are not repeated for every phenotype.

Constant phenotypes are excluded

Phenotypes with zero or NaN variance are removed before the scan. If none remain, jaxQTL writes no result blocks and records a warning.

See Trans output for filenames and schemas.