gemini - a lightweight db framework for exploring genetic variation.
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 following is a video of a high-level talk from SciPy 2013 describing GEMINI.