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Can I use the GDC Application Programming Interface (API) to retrieve data sets associated with visualizations?

Submitted by Anonymous on Wed, 06/07/2017 - 09:33

Yes. The GDC provides additional analysis endpoints to retrieve data sets associated with visualizations. Analysis endpoints include: survival, top_cases_counts_by_genes, top_mutated_genes_by_project, top_mutated_cases_by_gene, top_mutated_cases_by_ssm, and mutated_cases_count_by_project.

Please refer to the GDC API User's Guide Analysis Section for additional information.

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How is survival analysis calculated?

Submitted by Anonymous on Tue, 06/06/2017 - 12:29

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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 Tue, 06/06/2017 - 12:21

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:

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Why are there some projects without data analysis and visualization features?

Submitted by Anonymous on Tue, 06/06/2017 - 12:18

Data analysis and visualization features are only available for projects which maintain open-access MAF files. Programs such as TARGET maintain controlled-access MAF files only. As such, data analysis and visualization cannot be applied to TARGET projects.