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If the resource file indicates that there are more than one trait, then Eqtl will try to estimate positions and additive effects for all the traits. This will happen even if no analysis was done on the extra traits. The output file will then have some null estimates.

When doing a jackknife with Zmapqtl, the user should check that the file ending in the letter i is truely the last version of the interim jackknife file. Zmapqtl switches between a file ending in i and another ending in j, so check both and move the j file onto the i file if required.

If you set the significance threshold too high, then Eqtl may find no QTL in the qtlcart.z output. If this is the case, then Eqtl will crash.

Christopher Basten 2002-03-27