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Command-line overview¤

Run jaxqtl COMMAND [OPTIONS]. Choose a command by the result you need:

Command Required inputs Result
cis Genotypes, phenotypes, covariates Lead association and gene-level adjusted p-value per tested phenotype.
nominal Genotypes, phenotypes, covariates Every association within each cis window.
trans Genotypes, phenotypes, covariates Associations across retained phenotypes and variants, written in chunks.
compute-pcs Expression matrix, component count Expression PCs and their explained-variance proportions.

Command reference¤

  • Mapping commands: input selection, covariates, offsets, tests, filters, and fitting controls.
  • Expression PCA: normalization, transformation, filtering order, component limits, and output files.
  • Output schemas: mapping result columns and PCA variance tables.

For complete workflows, start with the Quickstart or Compute expression PCs.

Help and option conventions¤

jaxqtl --help
jaxqtl cis --help
jaxqtl nominal --help
jaxqtl trans --help
jaxqtl compute-pcs --help

Options follow the subcommand. Help lists accepted values and defaults. Boolean flags such as --verbose take no value. Options accepting several names, such as --genes, accept comma- or space-delimited names; identifier files contain one ID per line without a header.

All commands support --seed (default 0), --platform (default cpu), and --verbose. GPU and TPU execution require a compatible JAX installation; see Installation.

Output paths¤

Mapping treats --out as a prefix (default jaxqtl) and adds command-specific result suffixes. Expression PCA treats it as a TSV filename (default jaxqtl.princ_comp.tsv) and adds .variance.tsv for its companion table. Every command writes a log at <out>.log.