GWAS steps (linear mixed model)

1. Imputation
    (QTLmax ▶ Preprocess ▶ Imputation)

2. PCA computation
    (QTLmax ▶ Genetic analytics ▶ Association ▶ Population studies ▶ ADMIXTURE)

3. Genetic similarity matrix computation
    (QTLmax ▶ Genetic analytics ▶ Association ▶ Population studies ▶ ADMIXTURE)

4. Merging phenotype and PCA tables
    (QTLmax Workbench ▶ Miscellaneous tools ▶ DataPro)

5. LMM-GWAS
    (QTLmax ▶ Genetic analytics ▶ Association ▶ Linear mixed model ▶ GWAS)

6. Genomic control (Use this in case that genomic inflation is observed.)
    (QTLmax ▶ Genetic analytics ▶ Association ▶ Genomic control)

7. Manhattan plotting
    (QTLmax Workbench ▶ Graph studio ▶ Manhattan plot)

8. QQ plotting
    (QTLmax Workbench ▶ Graph studio ▶ QQ plot)