Mining Genetic Variation in any Species with GEMINI

A fundamental analysis challenge in studying the genetic basis of traits is isolating the handful of variants underlying a phenotype from the sea of benign, irrelevant variants. Distinguishing one variant from another is effectively impossible without context. Recognizing this need and to provide a more powerful and integrated approach for variant interpretation, we have developed GEMINI (GEnome MINIng; gemini.readthedocs.org). GEMINI combines genetic variants with a diverse and adaptable collection of genome annotations (e.g., dbSNP, ExAC, UCSC, ClinVar, 1000 Genomes) into a unified database to facilitate variant interpretation in studies of human disease. By integrating variants with extensive genome annotations, as well as sample phenotypes and family structure, one can compose complex queries based on sample genotypes, inheritance patterns, and crucial genome annotations. Owing to these strengths, GEMINI is widely-used in studies of rare human diseases.

Here we present an optimized and much more general version of GEMINI. By providing built-in annotations for model organisms and also allowing users to specify the set of annotations that are germane to their species and study needs, GEMINI has been completely redesigned to support genetic research in any species. We will discuss the functionality that GEMINI enables and demonstrate its utility in studies of genetic traits in diverse species.