ArticleBioinformatics (Oxford, England)2015
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Mapping MAVE data for use in human genomics applications.Genome biology · 2025Article
- MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays.Genome biology · 2025Article
- REEV: review, evaluate and explain variants.Nucleic acids research · 2024Article
- SeqCAT: Sequence Conversion and Analysis Toolbox.Nucleic acids research · 2024Article
- Mapping MAVE data for use in human genomics applications.bioRxiv : the preprint server for biology · 2024Article
- Systematic errors in annotations of truncations, loss-of-function and synonymous variants.Frontiers in genetics · 2023Article
- When a Synonymous Variant Is Nonsynonymous.Genes · 2022Article
- A performance evaluation study: Variant annotation tools - the enigma of clinical next generation sequencing (NGS) based genetic testing.Journal of pathology informatics · 2022Article
- Pathogenic Abnormal Splicing Due to Intronic Deletions that Induce Biophysical Space Constraint for Spliceosome Assembly.American journal of human genetics · 2019Article
- [Detection and interpretation of somatic variants in molecular pathology].Der Pathologe · 2019Article
- GLIS Rearrangement is a Genomic Hallmark of Hyalinizing Trabecular Tumor of the Thyroid Gland.Thyroid : official journal of the American Thyroid Association · 2019Article
- BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.PLoS genetics · 2018Article
- hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.Human mutation · 2018Article
- KRAS mutation is predictive of outcome in patients with pulmonary sarcomatoid carcinoma.Histopathology · 2018Article
- VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.Human mutation · 2018Article
- Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.The Journal of molecular diagnostics : JMD · 2017Article
- A variant by any name: quantifying annotation discordance across tools and clinical databases.Genome medicine · 2017Article
- Towards precision medicine.Nature reviews. Genetics · 2016Review
- Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.BMC bioinformatics · 2016Article
- Human genotype-phenotype databases: aims, challenges and opportunities.Nature reviews. Genetics · 2015Review
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Authors and funding
6 authors.
Funding
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Abstract
unlabelledBiological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. AVAILABILITY AND IMPLEMENTATION: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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