  Beyond identifying genetic variants, we introduce a set of Boolean relations
that allows for a comprehensive classification of the relations for every pair
of variants by taking all minimal alignments into account. We present an
efficient algorithm to compute these relations, including a novel way of
efficiently computing all minimal alignments within the best theoretical
complexity bounds. We show that for variants of the CFTR gene in dbSNP these
relations are common and many non-trivial. Ultimately, we present an approach
for the storing and indexing of variants in the context of a database that
enables efficient querying for all these relations.
