TorchGWAS : GPU-accelerated GWAS for thousands of quantitative phenotypes
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arXiv
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| Auteurs principaux: | , , , , , , , |
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| Format: | Preprint |
| Publié: |
2026
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| _version_ | 1866914500746149888 |
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| author | Zhao, Xingzhong Xie, Ziqian Islam Saiful, Sheikh Muhammad Xia, Tian Chen Cheng Zhi, Degui |
| author_facet | Zhao, Xingzhong Xie, Ziqian Islam Saiful, Sheikh Muhammad Xia, Tian Chen Cheng Zhi, Degui |
| contents | Motivation: Modern bioinformatics workflows, particularly in imaging and representation learning, can generate thousands to tens of thousands of quantitative phenotypes from a single cohort. In such settings, running genome-wide association analyses trait by trait rapidly becomes a computational bottleneck. While established GWAS tools are highly effective for individual traits, they are not optimized for phenotype-rich screening workflows in which the same genotype matrix is reused across a large phenotype panel. Results: We present TorchGWAS, a framework for high-throughput association testing of large phenotype panels through hardware acceleration. The current public release provides stable Python and command-line workflows for linear GWAS and multivariate phenotype screening, supports NumPy, PLINK, and BGEN genotype inputs, aligns phenotype and covariate tables by sample identifier, and performs covariate adjustment internally. In a benchmark with 8.9 million markers and 23,000 samples, fastGWA required approximately 100 second per phenotype on an AMD EPYC 7763 64-core CPU, whereas TorchGWAS completed 2,048 phenotypes in 10 minute and 20,480 phenotypes in 20 minutes on a single NVIDIA A100 GPU, corresponding to an approximately 300- to 1700-fold increase in phenotype throughput. TorchGWAS therefore makes large-scale GWAS screening practical in phenotype-rich settings where thousands of quantitative traits must be evaluated efficiently. Availability and implementation: TorchGWAS is implemented in Python and distributed as a documented source repository at https://github.com/ZhiGroup/TorchGWAS. The current release provides a command-line interface, packaged source code, tutorials, benchmark scripts, and example workflows. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2604_21095 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | TorchGWAS : GPU-accelerated GWAS for thousands of quantitative phenotypes Zhao, Xingzhong Xie, Ziqian Islam Saiful, Sheikh Muhammad Xia, Tian Chen Cheng Zhi, Degui Distributed, Parallel, and Cluster Computing Software Engineering Genomics Motivation: Modern bioinformatics workflows, particularly in imaging and representation learning, can generate thousands to tens of thousands of quantitative phenotypes from a single cohort. In such settings, running genome-wide association analyses trait by trait rapidly becomes a computational bottleneck. While established GWAS tools are highly effective for individual traits, they are not optimized for phenotype-rich screening workflows in which the same genotype matrix is reused across a large phenotype panel. Results: We present TorchGWAS, a framework for high-throughput association testing of large phenotype panels through hardware acceleration. The current public release provides stable Python and command-line workflows for linear GWAS and multivariate phenotype screening, supports NumPy, PLINK, and BGEN genotype inputs, aligns phenotype and covariate tables by sample identifier, and performs covariate adjustment internally. In a benchmark with 8.9 million markers and 23,000 samples, fastGWA required approximately 100 second per phenotype on an AMD EPYC 7763 64-core CPU, whereas TorchGWAS completed 2,048 phenotypes in 10 minute and 20,480 phenotypes in 20 minutes on a single NVIDIA A100 GPU, corresponding to an approximately 300- to 1700-fold increase in phenotype throughput. TorchGWAS therefore makes large-scale GWAS screening practical in phenotype-rich settings where thousands of quantitative traits must be evaluated efficiently. Availability and implementation: TorchGWAS is implemented in Python and distributed as a documented source repository at https://github.com/ZhiGroup/TorchGWAS. The current release provides a command-line interface, packaged source code, tutorials, benchmark scripts, and example workflows. |
| title | TorchGWAS : GPU-accelerated GWAS for thousands of quantitative phenotypes |
| topic | Distributed, Parallel, and Cluster Computing Software Engineering Genomics |
| url | https://arxiv.org/abs/2604.21095 |