**Eqtl** essentially finds the peaks in the likelihood ratio graph of the results from **Zmapqtl**. It
goes along the chromosome, and determines whether the likelihood ratio test
statistic is increasing or decreasing. Upon a change, it picks out the position
and estimates of other parameters. The user can specify that the peaks of
interest need be higher than some ``Significance threshold'' to be considered QTLs.
The default is 3.84, that is, any peak that is less than 3.84 is ignored. This
can be changed with the **-S** option. If you have run **Zmapqtl** and done a
permutation test,
**Eqtl** automatically reads the output and sets the significance threshold subject to
the value of the size, set with the **-a** option. For a size of , the
the -percentile is calculated from the experimentwise test values.

The final option is a flag to output LOD scores rather than likelihood ratios. The default
behavior of the ** QTL Cartographer** system is to use a likelihood ratio test statistic (LR)
rather than a LOD score. For a hypotheses , let be the
likelihood of the data given the hypothesis. For a pair of hypotheses and , this
would yield and . The LOD score is defined as

The likelihood ratio test statistic (LR) is

and thus