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Published June 5, 2025 | Version v1.61
Software Open

wtsi-hgi/QTLight: QTLight v1.61 – Flexible eQTL Mapping with LIMIX, TensorQTL, and SAIGE-QTL

Authors/Creators

  • 1. Wellcome Sanger Institute | University of Cambridge | University of Manchester
  • 2. @sanger @opentargets

Description

Highlights

This release introduces improved flexibility for genotype PCA control, streamlined input support, and a more efficient modular design.

Added

  • Support for predefined genotype PCs for both bulk and single-cell workflows.
  • Improved dynamic PC selection and pruning logic.
  • Better compatibility with both .vcf and .pgen/.bed genotypes.
  • Modular entry points for LIMIX, TensorQTL, and SAIGE-QTL modes.

Fixed

  • Input parsing errors and phenotype/VCF matching issues.
  • Normalization inconsistencies in mixed sample categories.

Dependencies

  • Python ≥ 3.8
  • Nextflow ≥ 22.04
  • Tools: TensorQTL, LIMIX, SAIGE-QTL, PLINK2, bcftools

Citation

Ozols, M., Cuomo, A., Bonder, M. J., Ponstingl, H., Alegbe, T., Harris, B., & Jang, H. (2025). QTLight: Quantitative Trait Loci mapping pipeline (Version v1.61) [Computer software]. https://github.com/wtsi-hgi/QTLight

Files

wtsi-hgi/QTLight-v1.61.zip

Files (286 Bytes)

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Additional details

Related works

Is supplement to
Software: https://github.com/wtsi-hgi/QTLight/tree/v1.61 (URL)

Software

Repository URL
https://github.com/wtsi-hgi/QTLight