Hgvs: A Python Package for Manipulating Sequence Variants Using HGVS Nomenclature: 2018 Update

Overview

Journal Hum Mutat

Specialty Genetics

Date 2018 Aug 22

PMID 30129167

Citations 11

Authors

Meng Wang

Keith M Callenberg

Raymond Dalgleish

Alexandre Fedtsov

Naomi K Fox

Peter J Freeman

Kevin B Jacobs

Piotr Kaleta

Andrew J McMurry

Andreas Prlic

Veena Rajaraman

Reece K Hart

Affiliations

Soon will be listed here.

Abstract

The Human Genome Variation Society (HGVS) nomenclature guidelines encourage the accurate and standard description of DNA, RNA, and protein sequence variants in public variant databases and the scientific literature. Inconsistent application of the HGVS guidelines can lead to misinterpretation of variants in clinical settings. Reliable software tools are essential to ensure consistent application of the HGVS guidelines when reporting and interpreting variants. We present the hgvs Python package, a comprehensive tool for manipulating sequence variants according to the HGVS nomenclature guidelines. Distinguishing features of the hgvs package include: (1) parsing, formatting, validating, and normalizing variants on genome, transcript, and protein sequences; (2) projecting variants between aligned sequences, including those with gapped alignments; (3) flexible installation using remote or local data (fully local installations eliminate network dependencies); (4) extensive automated tests; and (5) open source development by a community from eight organizations worldwide. This report summarizes recent and significant updates to the hgvs package since its original release in 2014, and presents results of extensive validation using clinical relevant variants from ClinVar and HGMD.

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