GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

DSpace/Manakin Repository

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

Citable link to this page


Title: GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
Author: Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

Note: Order does not necessarily reflect citation order of authors.

Citation: Paila, Umadevi, Brad A. Chapman, Rory Kirchner, and Aaron R. Quinlan. 2013. “GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations.” PLoS Computational Biology 9 (7): e1003153. doi:10.1371/journal.pcbi.1003153.
Full Text & Related Files:
Abstract: Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.
Published Version: doi:10.1371/journal.pcbi.1003153
Other Sources:
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at
Citable link to this page:
Downloads of this work:

Show full Dublin Core record

This item appears in the following Collection(s)


Search DASH

Advanced Search