HaploTypo: a variant-calling pipeline for phased genomes
| Autor: | Manuel Molina, Laia Carreté, Verónica Mixão, Toni Gabaldón, Cinta Pegueroles |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Statistics and Probability
Heterozygote Computer science Computational biology Biochemistry Genome 03 medical and health sciences 0302 clinical medicine Genetic variation Molecular Biology 030304 developmental biology computer.programming_language Supplementary data 0303 health sciences Haplotype Genetic variants Python (programming language) Genome Analysis Pipeline (software) Applications Notes Computer Science Applications Computational Mathematics Computational Theory and Mathematics Haplotypes computer 030217 neurology & neurosurgery Software Reference genome |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | 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. 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). |
| Databáze: | OpenAIRE |
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