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GEMINI - integrative exploration of genetic variation and genome annotations.



Gemini is largely replaced by slivar. We recommend to update your pipelines and software to use slivar when possible. The installation is simpler and the tool is more flexible and includes extensive support for rare disease analysis


The intent of GEMINI (GEnome MINIing) is to provide a simple, flexible, and powerful framework for exploring genetic variation for personal and medical genetics. GEMINI is unique in that it integrates genetic variation (from VCF files) with a wealth of genome annotations into a unified database framework. Using this integrated database as the analysis framework, we aim to leverage the expressive power of SQL for data analysis, while attempting to overcome the fundamental challenges associated with using databases for very large (e.g. 1,000,000 variants times 1,000 samples yields one billion genotypes) datasets. In addition, by defining sample relationships with a PED file, GEMINI allows one to explore and test for variants that meet specific inheritance models (e.g., recessive, dominant, etc.).


The official documentation is here:

The following is a video of a high-level talk from SciPy 2013 describing GEMINI.


If you use GEMINI in your research, please cite the following manuscript:

Paila U, Chapman BA, Kirchner R, Quinlan AR (2013) GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS Comput Biol 9(7): e1003153. doi:10.1371/journal.pcbi.1003153


Mailing List

Questions and discussion should be directed to the following discussion list:!forum/gemini-variation


GEMINI is being developed in the Quinlan lab ( at the University of Utah and is led by Brent Pedersen, Uma Paila and Aaron Quinlan. Substantial contributions to the code base have also been made by Brad Chapman (@chapmanb) and Rory Kirchner (@roryk) at the Harvard School of Public Health.


Install GEMINI using the automated installation script, This script installs GEMINI along with required python libraries, third party tools and data files used for variant annotation. The installation documentation contains additional details on installed files and tools.


GEMINI is freely available under the MIT license.


GEMINI includes CADD scores (PMID: 24487276) for annotating variants.

CADD scores ( are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (

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