A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
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DOI：
10.1093/bioinformatics/btu630
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发表时间：
2015-01-15
期刊：
影响因子：
5.8
通讯作者：
Fusaro, Vincent A.
中科院分区：
文献类型：
--
作者：
Hart, Reece K.;Rico, Rudolph;Fusaro, Vincent A.
生物序列变异通常在科学文献、临床报告和变异数据库中使用人类基因组变异学会（HGVS）认可的突变命名指南表示。尽管该标准被广泛使用，但没有免费提供和全面的编程库。在这里，我们报告了一个开源且易于使用的Python库，该库根据HGVS规范促进了变体的解析，操作，格式化和验证。目前的实施集中在HGVS建议的子集上，该子集精确地描述了与高通量测序在临床诊断中的应用相关的序列水平变化。
Biological 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.