OpenVariant: a toolkit to parse and operate multiple input file formats
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- dc.contributor.author Martínez-Millán, David
- dc.contributor.author Brando, Federica
- dc.contributor.author Grau, Miguel L.
- dc.contributor.author Sánchez-Guixé, Mònica
- dc.contributor.author López Elorduy, Carlos
- dc.contributor.author Reyes-Salazar, Iker
- dc.contributor.author Deu-Pons, Jordi
- dc.contributor.author López Bigas, Núria
- dc.contributor.author González-Pérez, Abel
- dc.date.accessioned 2025-02-04T07:45:45Z
- dc.date.available 2025-02-04T07:45:45Z
- dc.date.issued 2024
- dc.description.abstract Summary: 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. Availability and implementation: OpenVariant is an open-source package available at https://github.com/bbglab/openvariant. Documentation may be found at https://openvariant.readthedocs.io.
- dc.description.sponsorship N.L.-B. acknowledges funding from the European Research Council [consolidator grant 682398]. This project has received funding from the European Union’s Horizon Europe programme [grant agreement CGI-Clinics 101057509]. IRB Barcelona is a recipient of a Severo Ochoa Centre of Excellence Award from the Spanish Ministry of Economy and Competitiveness (MINECO; Government of Spain) and an Excellence Institutional grant by the Asociación Española contra el Cancer, and is supported by CERCA (Generalitat de Catalunya). This work has also been funded by the Institute of Health Carlos III [project IMPaCT-Data, exp. IMP/00019], co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”).
- dc.format.mimetype application/pdf
- dc.identifier.citation Martínez-Millán D, Brando F, L Grau M, Sánchez-Guixé M, López-Elorduy C, Reyes-Salazar I, et al. OpenVariant: a toolkit to parse and operate multiple input file formats. Bioinformatics. 2024 Nov 28;40(12):btae714. DOI: 10.1093/bioinformatics/btae714
- dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btae714
- dc.identifier.issn 1367-4803
- dc.identifier.uri http://hdl.handle.net/10230/69474
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Bioinformatics. 2024 Nov 28;40(12):btae714
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/682398
- dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101057509
- dc.rights © The Author(s) 2024. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.other Seqüència de nucleòtids
- dc.subject.other Tumors
- dc.title OpenVariant: a toolkit to parse and operate multiple input file formats
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion