For design experiments (and others where there are three genotypic classes), various hypothesis tests can be performed. Recall that there are four hypotheses , , and that are explained in Section 3.4.4. Using -H with 10, 20, 30, 31 or 32 allows you to specify which likelihood ratio should be the basis for declaring QTL. Table 4.2 summarizes the output for various values used with the -H option.
Eqtl can process the results of running permutations, bootstraps and jackknives as well as of JZmapqtl. By default, Eqtl will only try to process the output of Zmapqtl and JZmapqtl. To change what Eqtl tries to process, use the -I option with a work code. This option takes a string as an argument, and each letter in the string tells Eqtl to do something. The default string is ZM, which indicates to process the single trait (Zmapqtl) and multi-trait (JZmapqtl) output. The letters PBJ tell Eqtl to process the permutation test, bootstrap and jacknife analysis files as well. Any combination of PBJZM may be used as the work code, but if P is to be used, then put it first because order of processing is the same as the order of the letters.