GISTIC (copy number driver detection)

GISTIC2.0, from Mermel and colleagues at the Broad Institute, facilitates sensitive and confident localisation of the targets of focal somatic copy number alteration by scoring each genomic region on the frequency and amplitude of alteration across a cohort and assigning a false-discovery q-value; it distinguishes arm-level from focal events and reports peak regions. TCGA copy number papers report GISTIC peaks, and the gene-level thresholded calls (deep deletion, amplification) on cBioPortal come from it. The Broad distributes it under a research licence, so OnCo's open-source map lists it as skipped.