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This is under active development at the moment, it will implemented in next version 2.0.0 |
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
- Sample
- Stats Knockout
- Distance matrixPopulation stratification (PCA)
- Identity-by-state (IBS) test
Population stratificationPrincipal component analysis (PCA) - Genome wide association studies (GWAS)Fisher testChi square test
- Family-based association analysis Transmission disequilibrium test (TDT)
Knockout Analysis
PCA
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.
Table of Contents:
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