Next Generation HGVS Nomenclature Checker

ABSTRACT Motivation Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Results Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description. Availability Mutalyzer is an Open Source project under the GNU Affero General Public License. The source code is available on GitHub (https://github.com/mutalyzer/mutalyzer) and a running instance is available at: https://mutalyzer.nl.

Mutalyzer 2: Next Generation HGVS Nomenclature Checker

Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description.