1. A computer-implemented method of increasing the speed of annotating variants from a plurality of subjects, the method comprising: receiving a plurality of variant files, the plurality of variant files comprising a plurality of variant lists for a corresponding plurality of subjects, the plurality of variant lists comprising variants found in a plurality of whole or partial genome sequences of the corresponding plurality of subjects, wherein the variants in the lists comprise one or more Single Nucleotide Polymorphisms (SNP), Deletions, Insertions, or Block Substitutions; identifying variants in common between multiple variant lists of the received plurality of variant files to identify multiple instances of at least one variant present in the variant lists; eliminating all but one instance of the at least one identified variant having multiple instances in the variant lists and combining the plurality of variant files to form a batch variant file comprising a plurality of variants, wherein the identified at least one variant having multiple instances in the received plurality of variant files is included only once the plurality of variants that form the batch variant file; generating annotations with an annotation processing system for the plurality of variants that form the batch variant file, and storing in an annotation database only one instance of each different annotated variant produced by the annotation processing system.
6. The method of claim 1 , further comprising defining a plurality of groups of annotation types, the groups comprising different annotation types from each other.