If the qtlcart.rc file if it exists, Permute.pl will first set its parameter values from
that file. Any command line options will override the qtlcart.rc values. If a parameter
has not been set by either the qtlcart.rc file or command line parameters, default values are
This option requires an email address. The temporary log file will be sent to
this address to indicate that the bootstrap is complete. If blank, then no email
message will be sent. The default is not to use this option.
Use this option to specify which trait to analyze. If there are t traits, then a value greater than
zero and less than or equal to t will cause Zmapqtl to be used. Otherwise, JZmapqtl will be used.
The default is 1. Note that using this option with a negative value will set this option to 1.
requires no operand. This tells Permute.pl to save the permuted datasets and their analytical results.
If used with a large number of permutations, a great deal of harddisk space will be used up. It is mainly
for debugging purposes.
requires no operand. This is the Unger flag. If used, then the script will also calculate
the sum and sum of squares for each permutation over the entire genome, and for each site over
all permutations. These values will be saved to files that can be processed with
RCpermute.pl to calculate site and permutation means and variances.
requires no operand. This is the Doust flag. If used, then the script will also calculate
the sum and sum of squares for the GxE scores. It was put in at the request of Andrew Doust.
It only works with JZmapqtl and models 14 or 34.
Will assume that the QTL Cartographer programs are in /usr/local/bin.
It will use interval mapping and do 500 permutations. Note that you need to
do an initial Zmapqtl run before beginning the permutation test. This initial
run will have created a qtlcart.rc file that contains the model and stem information.
If your computer went down during the permutation run, you can pick up where you
left off. Suppose that Permute.pl had finished 323 permutations in the above
example. You would observe a file mletest.z3.cwt.323 in the current working
directory. You could then run
% Permute.pl -b /usr/local/bin -c 4 -r 500 -a 323
to continue with the permutation test starting at the 324th iteration and
finishing with iteration 500.
Suppose we have another data set with multiple traits: The map is in
multitest.map and the data in multitest.cro. Further suppose that this
data set has four traits and it is a backcross. As above, assume that the
binaries are in /usr/local/bin.
Will use all the traits in a multitrait analysis and permute the data 500 times.
The likelihood ratio in the multitest.z0 file will be the focus of the test.
We need to specify column 5 for use with JZmapqtl.
The -s option allows you to save the permuted datasets and analytical results.
For iteration i, model m, filename stem qtlcart and single trait analysis,
there will be files qtlcart.cro.i, qtlcart.zm.i and qtlcart.zm.cwt.i.
For multitrait analysis, the qtlcart.cro.i will be saved along with the
set of trait analysis files qtlcart.zt.i, where t is
This option is mainly for debugging purposes.
Be aware that a large number of permutations will use a great deal of disk space.
You could modify the Permute.pl script to compress these files to save disk