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hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update
Author(s) -
Wang Meng,
Callenberg Keith M.,
Dalgleish Raymond,
Fedtsov Alexandre,
Fox Naomi K.,
Freeman Peter J.,
Jacobs Kevin B.,
Kaleta Piotr,
McMurry Andrew J.,
Prlić Andreas,
Rajaraman Veena,
Hart Reece K.
Publication year - 2018
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.23615
Subject(s) - python (programming language) , biology , computer science , computational biology , nomenclature , software , parsing , bioinformatics , artificial intelligence , programming language , taxonomy (biology) , botany
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.