PYRAMA: an open-source tool for advanced meta-analysis of genome wide association studies.

Georgios A Manios, Sophia Nteli, Panagiota I Kontou, Pantelis G Bagos

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Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

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4 authors.

Georgios A ManiosDepartment of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35131, Greece.

Sophia NteliDepartment of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35131, Greece.

Panagiota I KontouDepartment of Mathematics, University of Thessaly, Lamia 35131, Greece.

Pantelis G BagosDepartment of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35131, Greece.ORCID 0000-0003-4935-2325

Funding

European Union-NextGeneration EU

6 · The paper itself

Abstract

motivationGenome-wide association study (GWAS) meta-analysis tools are essential for integrating summary statistics across multiple cohorts, thereby increasing statistical power and validating genetic associations. Widely cited tools, such as METAL, PLINK, and GWAMA, have facilitated numerous significant discoveries in the field of GWAS. Nevertheless, these tools offer a limited set of meta-analysis methods and typically require users to have prior experience with command-line tools to be executed.

resultsWe present here PYRAMA, an open-source tool which is designed for meta-analysis of genome wide association studies. This work introduces an easy-to-use software package that includes several meta-analysis methods that are absent in similar software packages. PYRAMA is faster compared to other tools, supports robust methods for analysis and meta-analysis, fixed-effects, random-effects and Bayesian meta-analysis and it is currently the only tool that supports meta-analysis with imputation of summary statistics. It is available both as a standalone tool and as a freely available web server. AVAILABILITY AND IMPLEMENTATION: https://github.com/pbagos/PYRAMA, https://doi.org/10.5281/zenodo.17830449.

Indexed as

Genome-Wide Association StudyMeta-Analysis as TopicSoftwareBayes TheoremHumans

Identifiers

PMID41627853

DOI10.1093/bioinformatics/btag054

PMCPMC12925247

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.