Model 6

For Model 6, be sure to run SRmapqtl first. Once done, JZmapqtl will use all markers for specified traits that have rank as good or better than specified with the -n option.

You might also want to edit the SRmapqtl.out file prior to running JZmapqtl with model 6. You could pick out the top two or three ranked markers for each trait to be absolutely certain of which markers are being used as cofactors.