13. The system of claim 10 , wherein the annotation controller tracks which file identifiers are associated with which variants that will be annotated.
13. The system of claim 10 , wherein the annotation controller tracks which file identifiers are associated with which variants that will be annotated. 14. The system of claim 13 , wherein the annotation controller duplicates the annotation results for each of the multiple instances of the identified at least one variant having multiple instances for each of the received plurality of variant files that included the identified at least one variant having multiple instances.