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# GEMMA: Genome-wide Efficient Mixed Model Association | ||
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GEMMA is a software toolkit for fast application of linear mixed | ||
models and related models to genome-wide association studies (GWAS) | ||
and other large-scale data sets. | ||
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![Genetic associations discovered in CFW mice using GEMMA (Parker et al, | ||
Nat. Genet., 2016)](cfw.gif) | ||
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Features include: | ||
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+ Fast assocation tests implemented using the univariate linear mixed | ||
model (LMM). In GWAS, this can correct for account for population | ||
stratification and sample nonexchangeability. It also provides | ||
estimates of the proportion of variance in phenotypes explained (PVE) | ||
by available genotypes (often called "chip heritability" or "SNP | ||
heritability"). | ||
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+ Fast association tests for multiple phenotypes implemented using a | ||
multivariate linear mixed model (lvLMM). | ||
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It fits a multivariate linear mixed model (mvLMM) for testing marker | ||
associations with multiple phenotypes simultaneously while controlling | ||
for population stratification, and for estimating genetic correlations | ||
among complex phenotypes. | ||
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+ It fits a Bayesian sparse linear mixed model (BSLMM) using Markov | ||
chain Monte Carlo (MCMC) for estimating PVE by typed genotypes, | ||
predicting phenotypes, and identifying associated markers by jointly | ||
modeling all markers while controlling for population structure. | ||
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+ It estimates variance component/chip heritability, and partitions it | ||
by different SNP functional categories. In particular, it uses HE | ||
regression or REML AI algorithm to estimate variance components when | ||
individual-level data are available. It uses MQS to estimate variance | ||
components when only summary statisics are available. | ||
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*Add note here about posting questions, comments or bug reports to | ||
Issues.* | ||
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### Citing GEMMA | ||
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*Add text here.* | ||
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### License | ||
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Copyright (C) 2012–2017, Xiang Zhou. | ||
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### Quick start | ||
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*Add text here.* | ||
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### Setup | ||
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*Add text here.* | ||
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