OpenCGA provides an Analysis Framework that allows the implementation of Native Analysis and Wrapped Analysis. Native analysis are written in Java and make use of the OpenCGA APIs developed, this allow a fast implementation and the best scalability and performance. Users can develop native analysis outside the OpenCGA as a plugin. Wrapped Analysis act as connectors to external binaries that can be implemented in any language.

Analysis Framework

Native 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.

Variant analysis

Variant Analysis aims to implement the most common genetic analysis, at the moment are implemented:

• Variant Stats
• Sample Stats
• Genome-Wide Association Study
• Basic statistics
• Knockout Analysis
• Sample Eligibility Analysis

Clinical Interpretation Analysis

Clinical Interpretation Analysis allow to to discover variants or genes involved in 

• Primary Findings
• Secondary Findings

Custom Analysis (plugins)

User can easily install Native Analysis implemented externally to OpenCGA source code. We are considering creating a repository for the users. Tutorial is coming soon.

Wrapped 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.