A Boolean algebra for genetic variants

MotivationBeyond identifying genetic variants, we introduce a set of Boolean relations, which allows for a comprehensive classification of the relations of 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.ResultsWe show that these relations are common, and many non-trivial, for variants of the CFTR gene in dbSNP. 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.Availability and implementationA Python implementation is available at as well as an interface at .

Automated summary

In this study, a set of Boolean relations is introduced to comprehensively classify the relations of every pair of variants by considering all minimal alignments. An efficient algorithm is presented to compute these relations, with a novel method to compute all minimal alignments within the best theoretical complexity bounds. The study demonstrates the commonness and complexity of these relations for variants of the CFTR gene in dbSNP. Additionally, an approach for storing and indexing variants in a database is proposed, enabling efficient querying for all these relations.