GEMMA pipeline

GEMMA specifications


Unique identifier OMICS_25985
Alternative name Genome-wide Efficient Mixed Model Association
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.96
Stability Stable
Maintained Yes



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  • person_outline Matthew Stephens <>
  • person_outline Xiang Zhou <>

Publication for Genome-wide Efficient Mixed Model Association

GEMMA IN pipelines

PMCID: 5845532
PMID: 29559957
DOI: 10.3389/fendo.2018.00075

[…] was observed between two models (26). the covariates of age and body mass index (bmi) were adjusted for in the analysis., the association of sua level with snp genotypes was tested using the gemma (25). the covariates of age, sex, bmi, and the first five principle components were adjusted for in the model fitting. the conventional genome-wide significance level of p < 5 × 10−8 […]

PMCID: 5470659
PMID: 28614352
DOI: 10.1371/journal.pone.0176932

[…] loci in the same ld interval (true positives), and the window size of this range was set as 100,000 bp. simulated phenotypes were generated using gapit [29]. the mixed linear model was performed in gemma [23] and compared to analysis of the same simulated phenotype data using farmcpu., the norberg angle (101.8±sd = 9.8°) was averaged over both hips of 921 dogs belonging to 69 pure and 121 mixed […]

PMCID: 5611747
PMID: 28892072
DOI: 10.1038/tp.2017.183

[…] nrg1, nrg3, bace1 and psenen; fdr p<0.05) (supplementary figure 2), and signal for nd diagnosis in erbb4 (fdr p=0.002 for rs13385826) (supplementary figure 3)., association tests performed with gemma identified a signal for nw symptom count in erbb4 (fdr p=0.008, β=−0.517 for rs13001305, and for three highly correlated snps: rs73989053, rs13006797, rs17328083) (figure 1), suggesting […]

PMCID: 4537268
PMID: 26274327
DOI: 10.1371/journal.pone.0134865

[…] [29] using impute2 [30] and filtered (maf<0.05, impute info value < 0.8)[26]., a gwas analysis on the full cohort of twins using as as the phenotype was implemented using the program gemma [31]. the analysis used age as a covariate and also incorporated the family structure of the twins (see fig 1a and 1b, table 1)., samples were prepared for sequencing with the illuminatruseq […]

PMCID: 4564946
PMID: 26014426
DOI: 10.1038/ejhg.2015.102

[…] africans and 286 asians to improve the quality of imputation, particularly at lower frequency variants.14, we performed a linear mixed-model gwas analysis for each of the hormones using the program gemma,15 which is capable of accounting for relatedness of the study subjects when applicable, as well as population stratification and cryptic relatedness. association statistics using the score […]

GEMMA institution(s)
Department of Human Genetics, University of Chicago, Chicago, IL, USA; Department of Statistics, University of Chicago, Chicago, IL, USA
GEMMA funding source(s)
Supported in part by NIH grant HL092206 and NIH grant HG02585.

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