Pegueroles Queralt, Maria CintaMixão, VerónicaCarreté Muñoz, Laia, 1990-Molina, ManuelGabaldón Estevan, Juan Antonio, 1973-2020-05-142020-05-142020Pegueroles 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/btz9331367-4803http://hdl.handle.net/10230/44539SUMMARY: 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.application/pdfeng© 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.cominfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/bioinformatics/btz933Genome analysisinfo:eu-repo/semantics/openAccess