Changes

* '''Markers in PED and DAT file must be sorted by chromosome and position.'''

* '''Markers in PED and DAT file must be sorted by chromosome and position.'''

* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file.

* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file. Note that you must specify <code>--makeResiduals</code> in order to adjust the covariates out of the phenotype. See [[RAREMETALWORKER#Example_Command_Lines | Example Command Lines]] for examples and [[RAREMETALWORKER_command_reference#Trait_Options | Trait Options]] for more information.

==== VCF File ====

==== VCF File ====