If the qtlcart.rc file if it exists, Bootstrap.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.
requires no operand. This tells Bootstrap.pl to save the bootstrapped datasets and their analytical results.
If used with a large number of bootstraps, a great deal of harddisk space will be used up. It is mainly
for debugging purposes.
These commands assume that the QTL Cartographer programs are in /home/basten/bin.
It will use interval mapping and do 500 bootstrap iterations. Note that you need to
do an initial Zmapqtl run before beginning the bootstrap, and that initial run
will set the filename stem and the model for analysis.
If your machine crashed during the bootstrap analysis, then you can restart where you
left off (provided that the crash occurred during the Zmapqtl run). Suppose the
above completed 356 iterations and crashed during iteration 357. Then
% Bootstrap.pl -b /home/basten/bin -r 500 -a 356
would pick up the bootstrap at iteration 357 and complete at 500.
The -s option allows you to save the bootstrapped 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.bi.
This option is mainly for debugging purposes.
Be aware that a large number of iterations will use a great deal of disk space.
You could modify the Bootstrap.pl script to compress these files to save disk