Transcription of GEMMA User Manual
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GEMMA User Manual
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 .. 7. Missing Phenotypes .. 8. 2 Installing and Compiling GEMMA 9. 3 Input File Formats 10. PLINK Binary PED File Format .. 10. BIMBAM File Format .. 11. Mean Genotype File .. 11. Phenotype File .. 12. SNP Annotation File (optional) .. 12. Relatedness Matrix File Format .. 13. Original Matrix Format .. 13. Eigen Value and Eigen Vector Format .. 14. Covariates File Format (optional) .. 14. Beta/Z File .. 15. Category File .. 15. LD Score File .. 15. 1. 4 Running GEMMA 17. A Small GWAS Example Dataset.
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
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