I want to analyse prognosis of ovarian cancer patients according to the copy number variations of a specific region (e.g.8q24.11) in genome. Using TCGA level 3 CNV data I can run GISTIC and get the copy number of 8q24.21, which has the maximal amplification in ovarian cancer. But I don't know how to get the copy number of 8q24.11, which is less amplified in ovarian cancer. How can I adjust the parameter of GISTIC to get the copy number of 8q24.11 or should I download level 1 or level 2 CNV data of TCGA?
Thanks for any help.