Hi all,

I analyzed CNV in the population using GISTIC2 and have expected result.

Now, I would like to extract the gene count (reoccurring count) and associated q-value for that gene.

I tried to dig the standard output text file from GISTIC

wc -l *txt
  23110 all_data_by_genes.txt
    223   all_lesions.conf_75.txt
  23110 all_thresholded.by_genes.txt
    1152 amp_genes.conf_75.txt
  23110 broad_data_by_genes.txt
        41 broad_significance_results.txt
        41 broad_values_by_arm.txt
   1152 del_genes.conf_75.txt
  23110 focal_data_by_genes.txt
     17 sample_cutoffs.txt
     16 sample_seg_counts.txt

Can somebody please point out the files (perhaps combination of files) from where I could extract information.

If anybody have experience this, please share.

Thanks!