How copy number variation thresholds are defined in GISTIC
The best solution is to use only the broad alterations, using the file broad_values_by_arm.txt.

In particular, for each sample, the highest threshold is computed as the sum of the noise (low-level) threshold (e.g. 0.1) plus the maximum value of copy number variation for the sample over all the arms. Similarly, the lowest threshold is the minimum value for the sample over all the arms plus the negative noise (low-level) threshold (e.g. -0.1).