wtsi-hgi/QTLight: QTLight v1.61 – Flexible eQTL Mapping with LIMIX, TensorQTL, and SAIGE-QTL
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2025
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| _version_ | 1866902236831940608 |
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| author | Matiss Tobi Alegbe |
| author_facet | Matiss Tobi Alegbe |
| contents | <h2>Highlights</h2> <p>This release introduces improved flexibility for genotype PCA control, streamlined input support, and a more efficient modular design.</p> <h3><code>Added</code></h3> <ul> <li>Support for <strong>predefined genotype PCs</strong> for both bulk and single-cell workflows.</li> <li>Improved dynamic PC selection and pruning logic.</li> <li>Better compatibility with both <code>.vcf</code> and <code>.pgen/.bed</code> genotypes.</li> <li>Modular entry points for LIMIX, TensorQTL, and SAIGE-QTL modes.</li> </ul> <h3><code>Fixed</code></h3> <ul> <li>Input parsing errors and phenotype/VCF matching issues.</li> <li>Normalization inconsistencies in mixed sample categories.</li> </ul> <h3><code>Dependencies</code></h3> <ul> <li>Python ≥ 3.8</li> <li>Nextflow ≥ 22.04</li> <li>Tools: TensorQTL, LIMIX, SAIGE-QTL, PLINK2, bcftools</li> </ul> <h3><code>Citation</code></h3> <p>Ozols, M., Cuomo, A., Bonder, M. J., Ponstingl, H., Alegbe, T., Harris, B., & Jang, H. (2025). <em>QTLight: Quantitative Trait Loci mapping pipeline (Version v1.61)</em> [Computer software]. https://github.com/wtsi-hgi/QTLight</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15601494 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | wtsi-hgi/QTLight: QTLight v1.61 – Flexible eQTL Mapping with LIMIX, TensorQTL, and SAIGE-QTL Matiss Tobi Alegbe <h2>Highlights</h2> <p>This release introduces improved flexibility for genotype PCA control, streamlined input support, and a more efficient modular design.</p> <h3><code>Added</code></h3> <ul> <li>Support for <strong>predefined genotype PCs</strong> for both bulk and single-cell workflows.</li> <li>Improved dynamic PC selection and pruning logic.</li> <li>Better compatibility with both <code>.vcf</code> and <code>.pgen/.bed</code> genotypes.</li> <li>Modular entry points for LIMIX, TensorQTL, and SAIGE-QTL modes.</li> </ul> <h3><code>Fixed</code></h3> <ul> <li>Input parsing errors and phenotype/VCF matching issues.</li> <li>Normalization inconsistencies in mixed sample categories.</li> </ul> <h3><code>Dependencies</code></h3> <ul> <li>Python ≥ 3.8</li> <li>Nextflow ≥ 22.04</li> <li>Tools: TensorQTL, LIMIX, SAIGE-QTL, PLINK2, bcftools</li> </ul> <h3><code>Citation</code></h3> <p>Ozols, M., Cuomo, A., Bonder, M. J., Ponstingl, H., Alegbe, T., Harris, B., & Jang, H. (2025). <em>QTLight: Quantitative Trait Loci mapping pipeline (Version v1.61)</em> [Computer software]. https://github.com/wtsi-hgi/QTLight</p> |
| title | wtsi-hgi/QTLight: QTLight v1.61 – Flexible eQTL Mapping with LIMIX, TensorQTL, and SAIGE-QTL |
| url | https://doi.org/10.5281/zenodo.15601494 |