GEMMA User Manual

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GEMMA User Manual Xiang Zhou May 18, 2016. Contents 1 Introduction 4. What is GEMMA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4. How to Cite GEMMA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4. Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. Univariate Linear Mixed Model . . . . . . . . . . . . . . . . . . . . . . . . . . 5. Multivariate Linear Mixed Model . . . . . . . . . . . . . . . . . . . . . . . . . 5. Bayesian Sparse Linear Mixed Model . . . . . . . . . . . . . . . . . . . . . . . 6. Variance Component Models . . . . . . . . . . . . . . . . . . . . . . . . . . . 7. Missing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7. Missing Genotypes.

1 Introduction 1.1 What is GEMMA GEMMA is the software implementing the Genome-wide E cient Mixed Model Association al-gorithm [7] for a standard linear mixed model and some of its close relatives for genome-wide