An alternative way to do the permutation test is in a batch file. For composite interval mapping,
one might want to reselect the background markers with **SRmapqtl** in each permutation. To this
end, one would need to permute the traits, reselect the background markers and then run
the composite interval mapping. The pseudo code example in Section 2.4.2
shows how to do this without the **SRmapqtl** step.

In the bootstrap, new datasets are created from the original by sampling with
replacement. New datasets are the same size as the original. The statistics are
redone and printed out. See the section **Prune** as to how to do bootstrapping.

Jackknife resampling is performed by calculating (the sample size) new estimates of
the parameters: The th estimate is calculated by deleting individual
from the dataset. The standard deviation over these new estimates
provides an estimate of the standard deviation for the test
statistic and additive and dominance effects. You invoke the Jackknife by setting the
number of bootstraps to 2.
**Zmapqtl** uses two interim files to perform the jackknife.
If you are using Model 6 in **Zmapqtl** and your filename stem is qtlcart,
then these files will be called **qtlcart.z6i** and **qtlcart.z6j**. These
files contain the sum and sum of squares up to the previous and current iteration, as
**Zmapqtl** runs.
Initially, the qtlcart.z6i file contains columns of zeros: This is
the sum before any iterations are performed. Subsequently, **qtlcart.z6j** will contain
the interim state after each odd-numbered iteration, while **qtlcart.z6i**
will contain the state after each even-numbered iteration. If individual
has no trait data, then the th iteration will be skipped. For this reason, one
cannot be sure that the file ending in ``j'' is the last iteration for odd sample sizes.
It is best to look at both files at the conclusion of a jackknife experiment, and
rename the interim
file with the greater number of iterations to
qtlcart.z6i. It this is done, then **Eqtl** will recognize it and calculate the means
and sample standard deviations of the test statistic and effects.

To clarify the interim file names, we consider an example using Model 6 in **Zmapqtl**
and the default filename stem ``qtlcart''. Table 3.5 lists the
interim file names. **Eqtl** automatically looks
for files named **qtlcart.z6e**, **qtlcart.z6a** and **qtlcart.z6i**. These files
will be processed and the appropriate calculations done. **Eqtl** will overwrite the
**qtlcart.z6b** and **qtlcart.z6j** files after completing its calculations, so if you
want to save them, do so before running **Eqtl**. If you chose to use another model
(say model 3), then the ``6'' in the filenames of Table 3.5 would be a ``3''.