Process Overview

The is a high level summary of VAGrENTs variant processing.

1. Input variant list is parsed one variant at a time
2. A Variant object is instantiated
3. The Variant object is handed to an Annotator object
4. The Annotator object queries a TranscriptSource object for a list of Transcripts potentially affected by the Variant
5. The Annotator object compares the Variant to each Transcript in turn, generating an AnnotationGroup object
6. All AnnotationGroup objects are collated and optionally sent to one or more Bookmarker objects
7. The Bookmarker filters the AnnotationGroup objects, selects the one that best matches its rules and marks it.
8. AnnotationGroup objects are returned.