The NCI Genomic Data Commons (GDC) is a massive project to provide the Cancer Research community a repository and computational platform for researchers who need to better understand cancer, its cl

The GDC begins with integer-level estimates of absolute copy number generated by either the ASCAT or ABSOLUTE pipeline. To establish a baseline, an integer-valued sample ploidy is computed as follows: 

When a mutation overlaps multiple transcripts or genes, the GDC annotates all consequences in the all_effects column of the MAF file and in the CONSEQUENCE table on the Mutation Summary Page. One transcript is then selected as the default for detailed annotation and visualization where a single consequence is shown.