Postprocessing

Postprocessing

After running mtSet, the following script can be used to merge the result files and estimate the p-values (p-values are obtained by a parametric fit of the test statistics):

./mtSet_postprocess --resdir resdir --outfile outfile --manhattan_plot

where

• resdir is a pointer to the folder containing the result files of the analysis.
• outfile is the prefix of the two output files. outfile.perm lists the test statistics (first column) and p-values (second column) of the permutated windows. outfile.test contains the (index, chromosome, start position, stop position, SNP index, number of SNPs, test statistics and p-value) of each window. Each window is saved in one row.
• manhattan_plot is a flag. If set, a manhattan plot is saved in outfile.manhattan.jpg (default: False).