How is survival analysis calculated?
Submitted by Anonymous
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Analyze Data
In the Most Frequent Mutations table for the VEP impact score, which algorithm in the VEP is the GDC using to determine “H" or “M”?
Submitted by Anonymous
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The IMPACT is categorized by the Sequencing Ontology type of the variants that is also compatible to snpEff. The VEP IMPACT rating is a separate rating given for compatibility with other variant annotation tools (e.g. snpEff). Basically, each category is associated with a set of SO terms:
Why are there some projects without data analysis and visualization features?
Submitted by Anonymous
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Data analysis and visualization features are only available for projects which maintain open-access MAF files. Programs such as the Molecular Analysis for Therapy Choice (MATCH) trial maintain controlled-access MAF files only. As such, data analysis and visualization cannot be applied to MATCH projects.
From what data are mutation-based visualization features derived?
Submitted by Anonymous
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The mutation-based visualization features are derived from open-access MAF files produced by GDC variant-calling pipelines.