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== Download EMMAX ==
== Download EMMAX ==
The latest release of EMMAX can be downloaded at [http://www.sph.umich.edu/csg/kang/emmax/download/index.html EMMAX Download Page]
The latest release of EMMAX can be downloaded at [http://csg.sph.umich.edu//kang/emmax/download/index.html EMMAX Download Page]
== Key Instructions ==
== Key Instructions ==
Q. Which allele is effect allele?
Q. Which allele is effect allele?
A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 1 in the .tped file, it will be the effect allele (usually the major allele)
A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 2 in the .tped file, it will be the effect allele (usually the major allele)
=== Support for VCF format and Gene-level Burden Test ===
=== Support for VCF format and Gene-level Burden Test ===
Q. Between IBS and BN matrix, which one is preferred?
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.
A. We believe that BN matrix is more robust to construct the empirical kinship matrix. Also we recommend to use call rate 95% threshold and MAF threshold of 0.01 when preparing the data.
=== NaN in the kinship file ===
Q. I am observing a series of -nan in the kinship matrix. What is the problem?
A. Most likely, monomorphic SNPs would create such a problem. Typically, MAF threshold such as 1% is used.
=== Citing EMMAX ===
=== Citing EMMAX ===
