The GDC provides an array of interactive, web-based Analysis Tools for performing in-depth gene- and variant- level analyses. The workflow is cohort-centric, meaning analyses are specific to a researcher's cohort of interest.
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Documentation
Data Analysis Tools
The GDC provides interactive, cohort-centric tools for analyzing genomic and clinical data.
Data Analysis Policy
Policies and guidelines for appropriate use of data, are provided by the GDC whether open- or controlled- access.
Data Harmonization and Generation
The GDC developers best-in-practice pipelines for processing the most common molecular platforms. Variant calling, gene expression analysis, and other pipelines are implemented using software and algorithms selected in consultation with experts in the genomics community.
What’s New with GDC and Cancer Research
Cancer Research Highlights and Publications:
Does the GDC use common exomes across all whole exome platforms?
There is a variety of target capture kits used by different sequencing centers. Most of the whole exome capture kits share many common genomic regions, especially for cancer related genes; However, which exons are included is totally dependent on the vendor's library preparation kit. There are often more differences among capture regions from different Targeted-Sequencing/Panel data.
The name of the capture kit used is available from the GDC read group properties. However, the GDC does not distribute the BED files for the read groups associated with these capture kits because some of them are proprietary.
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