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Output Documentation

This document summarizes the outputs generated by the QTLight pipeline, which supports eQTL mapping using LIMIX, TensorQTL, JAXQTL, and SAIGE-QTL. Outputs are organized by method.

TensorQTL Outputs

Output directory: TensorQTL_eQTLS/<condition>/

Core Results

In each proc_4pcs/base_output/base/ directory:

  • Cis_eqtls_qval.tsv
    Final FDR-corrected cis-eQTLs (q-values).
  • Cis_eqtls.tsv
    All tested cis-eQTLs with nominal p-values.
  • Covariates.tsv
    Matrix of covariates used in the association testing.
  • Expression_Data.sorted.bed
    BED-format gene expression data used for TensorQTL input.

Nominal Association Results

In each OPTIM_pcs/base_output/base/ directory:

  • cis_nominal1.cis_qtl_pairs.<CHR>.tsv.gz
    Per-chromosome nominal cis-eQTL results (only if nominal pass was run).
  • Cis_eqtls.tsv, Cis_eqtls_qval.tsv, Covariates.tsv, Expression_Data.sorted.bed
    Same as above, replicated under optimization output for reference.

PC Optimization Outputs

In each OPTIM_pcs/base_output__base/ directory:

  • optimise_nPCs-FDR1.txt
    Optimal number of phenotype PCs per condition (based on eGene yield).
  • optimise_nPCs-FDR1.pdf
    Plot of FDR q-value vs. number of PCs.
  • optim_pcs.txt
    Summary of the optimization process and selected PCs.

Input Snapshot

In each OPTIM_input/base_output__base/ directory:

  • Cis_eqtls_qval.tsv, Covariates.tsv, Expression_Data.sorted.bed, fake_file.fq
    These reflect the exact inputs used during the optimized TensorQTL run.

Structure Summary

Each condition or phenotype-level directory may include:

  • OPTIM_input/ → raw input files used for QTL mapping
  • OPTIM_pcs/ → results from PC optimization, including:
    • optimise_nPCs-FDR*.pdf / .txt → plots and tables of eGene discovery vs. PC count
    • base_output/base/ → full nominal cis-QTL results per tested PC count (e.g., cis_qtl_pairs.*.tsv.gz, Cis_eqtls.tsv, Cis_eqtls_qval.tsv)
  • <n>pcs/ → final output using the selected number of phenotype PCs (e.g., 4pcs/, 6pcs/, etc.), containing only filtered results like Cis_eqtls.tsv, Cis_eqtls_qval.tsv, Covariates.tsv, and Expression_Data.sorted.bed

LIMIX Outputs

Output directory: Limix_eQTLS/<group1>__<group0>/<group2>/results_<group1>/

Primary Outputs

  • qtl_results_all.h5: All QTL statistics in HDF5 format.
  • snp_metadata_all.txt: Per-variant metadata (e.g. position, MAF, filtering).
  • feature_metadata_all.txt: Per-gene metadata used in QTL mapping.

FDR-Filtered Results

  • qtl_results_all_FDR_*.tsv: QTL results filtered at different FDR thresholds (e.g. 0.05, 0.01).

JAXQTL Outputs

Output directory: JAX_eQTLS/<group0>__<group1>__<group2>/

cis-QTL Results

  • OPTIM_PCs/<mode>/*cis_score.tsv.gz: Per-gene cis-QTL scores using a negative binomial model.
  • OPTIM_PCs/<mode>/*cis_qtl_pairs.*.parquet: Nominal QTL results in Parquet format.

Aggregated and Optimized Outputs

  • <group0>__<group1>__<group2>__<mode>__merged_cis_scores.tsv.gz: Combined cis-QTL results across all chunks.
  • results/optimise_nPCs-FDR<alpha>.txt: Optimal PC counts for each condition at the specified FDR.
  • results/optimise_nPCs-FDR<alpha>.pdf: PC vs eGene plots.

SAIGE-QTL Outputs

Output directory: Saige_eQTLS/<condition>/

Core cis-QTL Results

  • minimum_q_all_genes.tsv: Minimum q-value per gene after multiple testing.
  • ACAT_all.tsv: ACAT-combined p-values across all cis-variants per gene.
  • <chr>__<condition>__all_vars_genes.tsv.gz: Complete cis gene-variant association matrix.
  • <chr>__<condition>__gene_lambdas.tsv: Lambda inflation factors per gene.