NAME - Do a permutation analysis with Zmapqtl or JZmapqtl

SYNOPSIS  [-b bin] [-X stem] [-m model] [-r reps] [-e email] [-c column] 
      [-t trait] [-I ihypo] [-a atrep] [-s] [-u] [-h]

DESCRIPTION iterates using Prune and Zmapqtl or JZmapqqtl to determine significance thresholds based on permutation testing.


If the qtlcart.rc file if it exists, 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 set.

This option requires the path to the QTL Cartographer binaries and perl scripts. The default is ~/bin directory.

requires an integer to control how many bootstrap iterations you want to do. The default is 1000.

This option allows you to specify the filename stem. The default is qtlcart.

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.

This option allows you to specify the Zmapqtl model to use. The default is interval mapping (3).

Use this option to specify which column in the Zmapqtl output file should be processed. The default is 4.

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.

Use this option to specify the hypothesis test for JZmapqtl. The default is 10. It is ignored if Zmapqtl is used.

requires no operand. This tells 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 an integer operand indicating the last completed iteration. Useful if your machine crashed during the permutation test.

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 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.

requires no operand. If used, it prints a usage message and exits.


Suppose the files and mletest.cro are in the current working directory.

    % Zmapqtl -X mletest -M 3 -A -V 
    %  -b /usr/local/bin -c 4 -r 500

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 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

    %  -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 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.

    % JZmapqtl -X multitest -M 3 -t 5 -I 10 
    % -b /usr/local/bin  -c 5 -r 500 -I 10 -t 5

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, and For multitrait analysis, the qtlcart.cro.i will be saved along with the set of trait analysis files qtlcart.zt.i, where t is the trait.

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 script to compress these files to save disk space.


Zmapqtl(1), JZmapqtl(1), Prune(1),,,,


In general, it is best to contact us via email (

        Christopher J. Basten, B. S. Weir and Z.-B. Zeng
        Department of Statistics, North Carolina State University
        Raleigh, NC 27695-7566, USA
        Phone: (919)515-1934

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