A1 Refereed original research article in a scientific journal
VarSCAT: A computational tool for sequence context annotations of genomic variants
Authors: Wang Ning, Khan Sofia, Elo Laura L
Publisher: PUBLIC LIBRARY SCIENCE
Publication year: 2023
Journal: PLoS Computational Biology
Journal name in source: PLOS COMPUTATIONAL BIOLOGY
Journal acronym: PLOS COMPUT BIOL
Article number: e1010727
Volume: 19
Issue: 8
Number of pages: 26
ISSN: 1553-734X
eISSN: 1553-734X
DOI: https://doi.org/10.1371/journal.pcbi.1010727
Web address : https://doi.org/10.1371/journal.pcbi.1010727
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/181158858
The sequence contexts of genomic variants play important roles in understanding biological significances of variants and potential sequencing related variant calling issues. However, methods for assessing the diverse sequence contexts of genomic variants such as tandem repeats and unambiguous annotations have been limited. Herein, we describe the Variant Sequence Context Annotation Tool (VarSCAT) for annotating the sequence contexts of genomic variants, including breakpoint ambiguities, flanking bases of variants, wildtype/mutated DNA sequences, variant nomenclatures, distances between adjacent variants, tandem repeat regions, and custom annotation with user customizable options. Our analyses demonstrate that VarSCAT is more versatile and customizable than the currently available methods or strategies for annotating variants in short tandem repeat (STR) regions or insertions and deletions (indels) with breakpoint ambiguity. Variant sequence context annotations of high-confidence human variant sets with VarSCAT revealed that more than 75% of all human individual germline and clinically relevant indels have breakpoint ambiguities. Moreover, we illustrate that more than 80% of human individual germline small variants in STR regions are indels and that the sizes of these indels correlated with STR motif sizes. VarSCAT is available from .
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