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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Detalles Bibliográficos
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
Descripción
Sumario: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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