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HaploTypo: a variant-calling pipeline for phased genomes.

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.

SUBMITTER: Pegueroles C

PROVIDER: S-EPMC7178392 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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HaploTypo: a variant-calling pipeline for phased genomes.

Pegueroles Cinta C Mixão Verónica V Carreté Laia L Molina Manu M Gabaldón Toni T

Bioinformatics (Oxford, England) 20200401 8

<h4>Summary</h4>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.<h4>Availability and implementation</h4>HaploTypo is implemented in Python 2 ...[more]

PMID: 31834373

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