PerSVade: personalized structural variant detection in any species of interest

Structural variants (SVs) underlie genomic variation but are often overlooked due to difficult detection from short reads. Most algorithms have been tested on humans, and it remains unclear how applicable they are in other organisms. To solve this, we develop perSVade (personalized structural variat...

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Bibliographic Details
Published inGenome Biology Vol. 23; no. 1; pp. 1 - 175
Main Authors Schikora-Tamarit, Miquel Àngel, Gabaldón, Toni
Format Journal Article
LanguageEnglish
Published London BioMed Central 16.08.2022
BMC
Subjects
Accuracy
Automation
Copy number
Datasets
Eukaryotes
Genomes
Insects
Optimization
Parameter optimization
Short reads
Simulation
Software
Structural variants
Variant calling
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Summary:Structural variants (SVs) underlie genomic variation but are often overlooked due to difficult detection from short reads. Most algorithms have been tested on humans, and it remains unclear how applicable they are in other organisms. To solve this, we develop perSVade (personalized structural variation detection), a sample-tailored pipeline that provides optimally called SVs and their inferred accuracy, as well as small and copy number variants. PerSVade increases SV calling accuracy on a benchmark of six eukaryotes. We find no universal set of optimal parameters, underscoring the need for sample-specific parameter optimization. PerSVade will facilitate SV detection and study across diverse organisms.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02737-4