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bioRxiv · 10.64898/2026.07.22.740077

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses

Rodriguez, Z. B.·Guare, L.·Caruth, L.·Cardone, K. M.·Carson, C. C.·Cherlin, T.·Mohammed, S.·Gupta, H.·Kumar, R.·Keat, K.·Verma, S. S.·Verma, A.
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Abstract

SummaryElectronic health record (EHR)-linked biobanks generate unprecedented genomic and phenotypic datasets, but their scientific utility is constrained by data fragmentation across institutional silos and incompatible computing infrastructures, forcing researchers to rewrite ad-hoc scripts for each new environment. We present the PMBB Geno-Pheno Toolkit, a suite of modular Nextflow pipelines for biobank-scale association analyses. This note focuses on the toolkits SAIGE family of pipelines -- supporting genome-wide (GWAS), exome-wide (ExWAS), and phenome-wide (PheWAS) association testing -- together with the companion GWAMA and ExWAS meta-analysis pipelines that enable cross-biobank replication. All components are containerized (Docker/Apptainer) and orchestrated with Nextflow, allowing the same workflows to run unmodified on local HPC clusters, cloud platforms, and the All of Us Research Workbench. Complementary toolkit pipelines for PLINK-based GWAS, polygenic scoring, LD-based clumping, and phenotype harmonization are also available and briefly noted. AvailabilityThe PMBB Geno-Pheno Toolkit is freely available at https://github.com/PMBB-Informatics-and-Genomics/pmbb-geno-pheno-toolkit under MIT open-source license.

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Rodriguez, Z. B., Guare, L., Caruth, L., Cardone, K. M., Carson, C. C., Cherlin, T., Mohammed, S., Gupta, H., Kumar, R., Keat, K., Verma, S. S., Verma, A.. 2026-07-26. PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses. https://doi.org/10.64898/2026.07.22.740077

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