Changes

  % emmax -v -d 10 -t [tped_prefix] -p [pheno_file] -k [kin_file] -o [out_prefix]

  % emmax -v -d 10 -t [tped_prefix] -p [pheno_file] -k [kin_file] -o [out_prefix]

This will generate the following files:
 * [out_prefix].reml : REML output with 6 lines, where each line represents (1) Log-likelihood with variance component (2) Log-likelihood without variance component, (3) \delta = \sigma_e^2 / \sigma_g^2 (Ratio between variance parameters) (4) \sigma_g^2 (genetic variance parameter), and (5) \sigma_e^2 (residual variance parameter), and (6) The pseudo-heritability estimates
 * [out_prefix].ps : Each line consist of [SNP ID], [beta], [SE-beta], [p-value].

This will generate the following files:

* [out_prefix].reml : REML output with 6 lines, where each line represents  

##Log-likelihood with variance component  

##Log-likelihood without variance component

## \delta = \sigma_e^2 / \sigma_g^2 (Ratio between variance parameters)

## \sigma_g^2 (genetic variance parameter)

## sigma_e^2 (residual variance parameter)

## The pseudo-heritability estimates
. (Explained variance by the kinship matrix)

 

* [out_prefix].ps : Each line consist of  

## SNP ID

## SE(beta)

## p-value.

=== Incorporating Covariates ===

=== Incorporating Covariates ===