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 integrated 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.
The official documentation is here: http://gemini.readthedocs.org/en/latest/
Mailing List: https://groups.google.com/forum/?fromgroups#!forum/gemini-variation
GEMINI is being developed in the Quinlan lab (quinlanlab.org) at the University of Virginia and is led by 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, gemini_install.py
. 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.::
wget https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py
python gemini_install.py /usr/local /usr/local/share/gemini
If you don't have administrative (or sudo) priveleges on you machine, use the
--nosudo
option::
python gemini_install.py --nosudo ~/src ~/data/gemini
If using the --nosudo
option, you will need to add the gemini/bin
directory
that was created as part of the installation to your PATH.
The first directory specified (/usr/local
in the first example above) dictates
the directory in which the gemini software should be installed. The second
directory specified (/usr/local/share/gemini
in the first example above) specifies
the directory in which the gemini annotations files should be installed. NOTE that
these are rather large files (some > 1Gb).
The installation documentation has additional tips and tricks if you run into any problems downloading or using the installation script.
GEMINI
is freely available under the MIT license.