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A. Use [[EPACTS]] software pipeline for running EMMAX with VCF files, including the implementations of gene-level burden tests.
A. Use [[EPACTS]] software pipeline for running EMMAX with VCF files, including the implementations of gene-level burden tests.
=== Encoding Case-control Phenotypes ===
Q. I would like to run EMMAX for case-control phenotypes. How can I encode the phenotypes?
A. If you encode case/control to 2/1, you will be able to run case-control analysis. Because EMMAX is based on linear mixed model rather than generalized mixed model, the effect size (beta) would not be meaningful, but the p-values should be reliable (unless case/control counts are highly imbalanced).
=== IBS matrix or BN matrix? ===
Q. Between IBS and BN matrix, which one is preferred?
A. We believe that BN matrix is more robust to construct the empirical kinship matrix. But we recommend to use call rate 95% threshold and MAF threshold of 0.01 when preparing the data.
=== Citing EMMAX ===
=== Citing EMMAX ===
