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. ; 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).
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