Martínez-Millán David, Brando Federica, L Grau Miguel, Sánchez-Guixé Mònica, López-Elorduy Carlos, Reyes-Salazar Iker, Deu-Pons Jordi, López-Bigas Núria, González-Pérez Abel
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain.
Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.
Bioinformatics. 2024 Nov 28;40(12). doi: 10.1093/bioinformatics/btae714.
Advances in high-throughput DNA sequencing technologies and decreasing costs have fueled the identification of small genetic variants (such as single nucleotide variants and indels) across tumors. Despite efforts to standardize variant formats and vocabularies, many sources of variability persist across databases and computational tools that annotate variants, hindering their integration within cancer genomic analyses. In this context, we present OpenVariant, an easily extendable Python package that facilitates seamless reading, parsing and refinement of diverse input file formats in a customizable structure, all within a single process.
OpenVariant is an open-source package available at https://github.com/bbglab/openvariant. Documentation may be found at https://openvariant.readthedocs.io.
高通量DNA测序技术的进步和成本的降低推动了肿瘤中小基因变异（如单核苷酸变异和插入缺失）的识别。尽管在规范变异格式和词汇方面做出了努力，但在注释变异的数据库和计算工具中，仍存在许多变异性来源，这阻碍了它们在癌症基因组分析中的整合。在此背景下，我们展示了OpenVariant，这是一个易于扩展的Python包，它能在单个进程中以可定制的结构促进对多种输入文件格式进行无缝读取、解析和优化。
OpenVariant是一个开源包，可在https://github.com/bbglab/openvariant获取。文档可在https://openvariant.readthedocs.io找到。
