Analysis

There are several native variant analysis implemented in OpenCGA, these use internal the different internal APIs developed to provide a scalable and high-performance implementation. Occasionally, these analysis can store results in the variant storage to allow users to filter by them, for instance GWAS analysis can be stored and/or indexed for filtering.

The analysis available include:

• Variant Stats
• Sample Stats
• GWAS
• ...

External Analysis

You can use external tools using the wrapper analysis. Some tools are being implemented naively and available to all users.

• Plink

Customisation

Users can easily extend and customise OpenCGA for their analysis.