% Prune -m example.map -i example.cross -o exout
Puts the user into an interactive menu for eliminating traits, markers, etc.
% Prune -m example.map -i example.cross -o exout -b 1
The -b option creates a new sample from the old. The new sample is created by resampling the original sample with replacement. Phenotypes and genotypes are kept together. The new sample will have the same sample size as the old one. It will be written to exout.crb. No new map will be written.
% Prune -m example.map -i example.cross -o exout -b 5 -M 20.0
Here, the -b option tells Prune to selectively genotype. We specify 20.0 percent with the -M option meaning that those individuals with trait values falling in the lower and upper 10 percent tails are retained, and the middle 80 percent are removed.