Dear every body, I downloaded level 3 CNV data from TCGA (segmented files). I am going to use Gistic2 to identify recurrent CNVs ? There are some command line in different links for it. https://gatkforums.broadinstitute.org/firecloud/discussion/8254/gistic2-0 But I dont know where to download Gistic2 and where to run command line instructions??
I also checked this link: How to extract the list of genes from TCGA CNV data but runGAIA() function need a lot memory to run. and I got allocation error. It used 100 gig bite RAM in one minute.