HaploTypo: a variant-calling pipeline for phased genomes

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 analy...

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Autores principales: Pegueroles, Cinta, Mixão, Verónica, Carreté, Laia, Molina, Manu, Gabaldón, Toni
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178392/
https://www.ncbi.nlm.nih.gov/pubmed/31834373
http://dx.doi.org/10.1093/bioinformatics/btz933
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author Pegueroles, Cinta
Mixão, Verónica
Carreté, Laia
Molina, Manu
Gabaldón, Toni
author_facet Pegueroles, Cinta
Mixão, Verónica
Carreté, Laia
Molina, Manu
Gabaldón, Toni
author_sort Pegueroles, Cinta
collection PubMed
description 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.
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spelling pubmed-71783922020-04-28 HaploTypo: a variant-calling pipeline for phased genomes Pegueroles, Cinta Mixão, Verónica Carreté, Laia Molina, Manu Gabaldón, Toni Bioinformatics Applications Notes 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. Oxford University Press 2020-04 2019-12-13 /pmc/articles/PMC7178392/ /pubmed/31834373 http://dx.doi.org/10.1093/bioinformatics/btz933 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ 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
spellingShingle Applications Notes
Pegueroles, Cinta
Mixão, Verónica
Carreté, Laia
Molina, Manu
Gabaldón, Toni
HaploTypo: a variant-calling pipeline for phased genomes
title HaploTypo: a variant-calling pipeline for phased genomes
title_full HaploTypo: a variant-calling pipeline for phased genomes
title_fullStr HaploTypo: a variant-calling pipeline for phased genomes
title_full_unstemmed HaploTypo: a variant-calling pipeline for phased genomes
title_short HaploTypo: a variant-calling pipeline for phased genomes
title_sort haplotypo: a variant-calling pipeline for phased genomes
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178392/
https://www.ncbi.nlm.nih.gov/pubmed/31834373
http://dx.doi.org/10.1093/bioinformatics/btz933
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AT molinamanu haplotypoavariantcallingpipelineforphasedgenomes
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