In OpenCGA, secondary findings are the actionable variants for a given sample. And a Tier 3 is assigned to all reported events of those variants.
Implementation
The implementation is based on creating a variant query by setting the sample, study and the list of actionable variant identifiers. Remember that actionable variants depends on the study assembly, and it is managed by the OpenCGA actionable variant manager. Once built the query, the secondary findings analysis executes the query and creates reported variants with its reported events. ACMG values are computed and a Tier 3 is assigned to each reported event.
Input parameters
- Sample ID
- Study ID
- Assembly
Output results
- List of reported variants
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