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Structural variant calling: the long and the short of it

Mahmoud, M; Gobet, N; Cruz-Dávalos, DI; Mounier, N; Dessimoz, C; Sedlazeck, FJ; (2019) Structural variant calling: the long and the short of it. Genome Biology volume , 20 (1) , Article 246. 10.1186/s13059-019-1828-7. Green open access

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Abstract

Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution-giving rise to the differences within populations and among species. Nevertheless, characterizing SVs and determining the optimal approach for a given experimental design remains a computational and scientific challenge. Multiple approaches have emerged to target various SV classes, zygosities, and size ranges. Here, we review these approaches with respect to their ability to infer SVs across the full spectrum of large, complex variations and present computational methods for each approach.

Type: Article
Title: Structural variant calling: the long and the short of it
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s13059-019-1828-7
Publisher version: https://doi.org/10.1186/s13059-019-1828-7
Language: English
Additional information: © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).
Keywords: De novo assembly, Gene fusion, Hybrid, Long-read, Mapping, RNA-Seq, Short-read, Structural variant (SV) detection
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10086581
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