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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 on

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 on

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.

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