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MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from readsopen access

Authors
Schmidt, MarkusKutzner, Arne
Issue Date
Jul-2023
Publisher
BMC
Keywords
Nested SV; Complex SV; Alignment; MEMs; Seeds; Pan-genomes; Ambiguity
Citation
GENOME BIOLOGY, v.24, no.1, pp.1 - 27
Indexed
SCIE
SCOPUS
Journal Title
GENOME BIOLOGY
Volume
24
Number
1
Start Page
1
End Page
27
URI
https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/189658
DOI
10.1186/s13059-023-03009-5
ISSN
1474-7596
Abstract
Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. For various yeast genomes, we practically compute adjacency matrices of our graph model and demonstrate that they provide highly accurate descriptions of one genome in terms of another. An open-source prototype implementation of our approach is available under the MIT license at https://github.com/ITBE-Lab/MA .
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