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