HaploTypo: a variant-calling pipeline for phased genomes
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- dc.contributor.author Pegueroles Queralt, Maria Cinta
- dc.contributor.author Mixão, Verónica
- dc.contributor.author Carreté Muñoz, Laia, 1990-
- dc.contributor.author Molina, Manuel
- dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
- dc.date.accessioned 2020-05-14T06:49:06Z
- dc.date.available 2020-05-14T06:49:06Z
- dc.date.issued 2020
- dc.description.abstract SUMMARY: An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. AVAILABILITY AND IMPLEMENTATION: HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- dc.description.sponsorship This work was supported by the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 and Marie Sklodowska-Curie grant agreements N° 642095, and 747607; the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants ‘Centro de Excelencia Severo Ochoa’ SEV-2012-0208, and BFU2015-67107 co-founded by European Regional Development Fund (ERDF); the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857; and INB Grant (PT17/0009/0023—ISCIII-SGEFI/ERDF).
- dc.format.mimetype application/pdf
- dc.identifier.citation Pegueroles C, Mixão V, Carreté L, Molina M, Gabaldón T. HaploTypo: a variant-calling pipeline for phased genomes. Bioinformatics. 2020; 36(8):2569-71. DOI: 10.1093/bioinformatics/btz933
- dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btz933
- dc.identifier.issn 1367-4803
- dc.identifier.uri http://hdl.handle.net/10230/44539
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Bioinformatics. 2020; 36(8):2569-71
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/642095
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/747607
- dc.rights © The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.subject.keyword Genome analysis
- dc.title HaploTypo: a variant-calling pipeline for phased genomes
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion