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# GEMMA: Genome-wide Efficient Mixed Model Association
GEMMA is a software toolkit for fast application of linear mixed
models (LMMs) and related models to genome-wide association studies
(GWAS) and other large-scale data sets.
Check out [NEWS.md](NEWS.md) to see what's new in each GEMMA release.
Please post comments, feature requests or suspected bugs to
[Github issues](https://github.com/xiangzhou/GEMMA/issues).
Currently, GEMMA is supported for Mac OS X and Unix-alike platforms
(e.g., Linux). Windows is not currently supported. If you are
interested in helping to make GEMMA available on Windows platforms
(e.g., by providing installation instructions for Windows, or by
contributing Windows binaries) please post a note in the
[Github issues](https://github.com/xiangzhou/GEMMA/issues).
*(The above image depicts physiological and behavioral trait
loci identified in CFW mice using GEMMA, from [Parker et al, Nature
Genetics, 2016](https://doi.org/10.1038/ng.3609).)*
## Key features
1. Fast assocation tests implemented using the univariate linear mixed
model (LMM). In GWAS, this can correct for population structure and
sample nonexchangeability. It also provides estimates of the
proportion of variance in phenotypes explained by available genotypes
(PVE), often called "chip heritability" or "SNP heritability".
2. Fast association tests for multiple phenotypes implemented using a
multivariate linear mixed model (mvLMM). In GWAS, this can correct for
populations tructure and sample nonexchangeability jointly in multiple
complex phenotypes.
3. Bayesian sparse linear mixed model (BSLMM) for estimating PVE,
phenotype prediction, and multi-marker modeling in GWAS.
4. Estimation of variance components ("chip heritability") partitioned
by different SNP functional categories from raw (individual-level)
data or summary data. For raw data, HE regression or the REML AI
algorithm can be used to estimate variance components when
individual-level data are available. For summary data, GEMMA uses the
MQS algorithm to estimate variance components.
## Quick start
1. Download and install the software. *Give more details here.*
2. Work through the demo. *Give more details here.*
3. Read the manual and run `gemma -h`. *Give more details here.*
## Citing GEMMA
If you use GEMMA for published work, please cite our paper:
+ Xiang Zhou and Matthew Stephens (2012). [Genome-wide efficient
mixed-model analysis for association studies.](http://doi.org/10.1038/ng.2310)
*Nature Genetics* **44**, 821–824.
If you use the multivariate linear mixed model (mvLMM) in your
research, please cite:
+ Xiang Zhou and Matthew Stephens (2014). [Efficient multivariate linear
mixed model algorithms for genome-wide association
studies.](http://doi.org/10.1038/nmeth.2848)
*Nature Methods* **11**, 407–409.
If you use the Bayesian sparse linear mixed model (BSLMM), please cite:
+ Xiang Zhou, Peter Carbonetto and Matthew Stephens (2013). [Polygenic
modeling with bayesian sparse linear mixed
models.](http://doi.org/10.1371/journal.pgen.1003264) *PLoS Genetics*
**9**, e1003264.
And if you use of the variance component estimation using summary
statistics, please cite:
+ Xiang Zhou (2016). [A unified framework for variance component
estimation with summary statistics in genome-wide association
studies.](https://doi.org/10.1101/042846) *bioRxiv* 042846.
## License
Copyright (C) 2012–2017, Xiang Zhou.
The *GEMMA* source code repository is free software: you can
redistribute it under the terms of the
[GNU General Public License](http://www.gnu.org/licenses/gpl.html). All
the files in this project are part of *GEMMA*. This project is
distributed in the hope that it will be useful, but **without any
warranty**; without even the implied warranty of **merchantability or
fitness for a particular purpose**. See file [LICENSE](LICENSE) for
the full text of the license.
## Setup
There are two ways to install GEMMA: (1) download the precompiled
binaries, or (2) compiling GEMMA from source. The first option is much
simpler, and is therefore recommended
### Using precompiled binaries
### Building binaries from source
*We provide a simple Makefile which will need to be customized; please
see the comments at the top of the Makefile. Explain why we
automatically generate a Makefile using programs such as CMake or
Autotools.*
You will need a standard C/C++ compiler such as GNU gcc, as well as
[GSL](http://www.gnu.org/s/gsl) and
[LAPACK](http://www.netlib.org/lapack) libraries. You will need to
change the library paths in the Makefile accordingly.
## Credits
The *GEMMA* software was developed by:
[Xiang Zhou](http://www.xzlab.org)<br>
Dept. of Biostatistics<br>
University of Michigan<br>
2012-2017
Peter Carbonetto, Tim Flutre, Matthew Stephens and others have also
contributed to the development of this software.
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