TorchGWAS : GPU-accelerated GWAS for thousands of quantitative phenotypes

TL;DR

TorchGWAS is a GPU-accelerated framework enabling rapid large-scale GWAS analysis across thousands of phenotypes, significantly outperforming CPU-based tools.

Contribution

It introduces a GPU-based implementation of GWAS that dramatically increases throughput for phenotype-rich genomic screening workflows.

Findings

TorchGWAS completes 20,480 phenotypes in 20 minutes on a single GPU.

It achieves a 1700-fold increase in phenotype throughput compared to CPU-based methods.

Supports large datasets with millions of markers and tens of thousands of samples.

Abstract

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.