Genotyping structural variants in pangenome graphs using the vg toolkit.
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Peer-reviewed
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Article
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Abstract
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.
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Keywords
Genome, Fungal, Genomic Structural Variation, Genotyping Techniques, Saccharomyces cerevisiae, Software, Whole Genome Sequencing
Journal Title
Genome Biol
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Journal ISSN
1474-7596
1474-760X
1474-760X
Volume Title
21
Publisher
Springer Science and Business Media LLC
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Sponsorship
National Human Genome Research Institute (U54HG007990, U01HL137183, 2U41HG007234)
W. M. Keck Foundation (DT06172015)
Simons Foundation (SFLIFE# 35190)
W. M. Keck Foundation (DT06172015)
Simons Foundation (SFLIFE# 35190)