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:

• Basic statistics
  • Variant stats
  • Sample stats
  • Cohort stats
  • Family stats
    
    
• Distance matrix
  • Identity-by-state (IBS) test
    
    
• Population stratification
  • Principal component analysis (PCA)
    
    
• Genome wide association studies (GWAS)
  • Fisher test
  • Chi square test
    
    
• Family-based association analysis
  • Transmission disequilibrium test (TDT)

Wrapper Analysis

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

• Plink
• rv-tests

Customisation

Users can easily extend and customise OpenCGA for their analysis.