Analyze Data

This discrepancy is due to differences in the data processing pipelines used by the GDC and other genomic portals. At the GDC, gene-level CNVs are derived from a mix of standardized pipelines. For TCGA projects, the CNV values are prioritized in the following order: SNP6 ABSOLUTE (LiftOver) > SNP6 ASCAT3 > WGS AscatNGS > SNP6 ASCAT2. All of these workflows produce absolute integer copy number values. 

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. 

The GDC 2.4 Röntgen Release brings a range of new features aimed at enhancing data analysis and user experience.

STAR gene expression quantification excludes reads that are mapped to multiple different genes. This can cause some genes to appear with zero expression in the final counts, even if mapped reads are present in the raw data. 

The GDC is excited to announce the release of 8000+ new whole genome sequencing (WGS) variant calls as part of Data Release 42. Highlights of this release include:

The latest GDC 2.3 Pauling Release introduces several new features designed to enhance user experience and improve data analysis.

The NCI GDC Analysis Tool Challenge is a collaborative competition aimed at enhancing cancer research by integrating innovative analysis tools with the GDC.

To view the top frequently mutated genes for a cohort, first build a cohort using the Cohort Builder and then select the Mutation Frequency tool in the Analysis Center

In the GDC 2.2 McClintock Release, the following features have been released: