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

TL;DR

PYRAMA is a new open-source tool for combining genetic study results, offering more methods and easier use than existing tools.

Contribution

PYRAMA introduces a user-friendly, faster tool with novel meta-analysis methods, including summary statistic imputation.

Findings

PYRAMA supports fixed-effects, random-effects, and Bayesian meta-analysis methods.

It is the only tool that allows meta-analysis with imputation of summary statistics.

The tool is available as both a standalone application and a web server.

Abstract

Genome-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.

We 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.

https://github.com/pbagos/PYRAMA, https://doi.org/10.5281/zenodo.17830449.