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hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.

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posted on 2019-07-11, 08:53 authored by M Wang, KM Callenberg, R Dalgleish, A Fedtsov, NK Fox, PJ Freeman, KB Jacobs, P Kaleta, AJ McMurry, A Prlić, V Rajaraman, RK Hart
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.

Funding

The hgvs package was developed by Invitae and subsequently released under the Apache license. M.W. was initially supported by Google Summer of Code and bioinformatics.org in the summer of 2015. Development is currently supported by institutions through the contributions of the named authors. Funding Information: Wellcome Trust. Grant Number: 204801/Z/16/Z

History

Citation

Human Mutation, 2018, 39(12), pp. 1803-1813

Author affiliation

/Organisation/COLLEGE OF LIFE SCIENCES/Biological Sciences/Genetics and Genome Biology

Version

  • VoR (Version of Record)

Published in

Human Mutation

Publisher

Wiley for Human Genome Variation Society

eissn

1098-1004

Acceptance date

2018-08-13

Copyright date

2018

Available date

2019-07-11

Publisher version

https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23615

Notes

The hgvs package is available at github (https://github.com/biocommons/hgvs) under the Apache 2.0 open‐source license. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs) and easily installed ‘pip install hgvs’. Docker images are available at docker hub (https://hub.docker.com/r/biocommons/hgvs/). Extensive documentation is available (https://hgvs.readthedocs.io/en/master/index.html).

Language

en

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