Jointly benchmarking small and structural variant calls with vcfdist Article Swipe
Tim Dunn
,
Justin M. Zook
,
James Holt
,
Satish Narayanasamy
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1186/s13059-024-03394-5
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1186/s13059-024-03394-5
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a joint evaluation of small and structural variants uniformly reduces measured errors for SNPs (− 28.9%), INDELs (− 19.3%), and SVs (− 52.4%) across three datasets. vcfdist also corrects a common flaw in phasing evaluations, reducing measured flip errors by over 50%. Lastly, we show that vcfdist is more accurate than previously published works and on par with the newest approaches while providing improved result interpretability.
Related Topics
Concepts
Interpretability
Indel
Benchmarking
Biology
Single-nucleotide polymorphism
Computational biology
Genetics
Phaser
Genome
1000 Genomes Project
Structural variation
Data mining
Computer science
Artificial intelligence
Gene
Genotype
Engineering
Business
Marketing
Electrical engineering
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1186/s13059-024-03394-5
- OA Status
- gold
- Cited By
- 4
- References
- 48
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4403075345
All OpenAlex metadata
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https://openalex.org/W4403075345Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1186/s13059-024-03394-5Digital Object Identifier
- Title
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Jointly benchmarking small and structural variant calls with vcfdistWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-10-02Full publication date if available
- Authors
-
Tim Dunn, Justin M. Zook, James Holt, Satish NarayanasamyList of authors in order
- Landing page
-
https://doi.org/10.1186/s13059-024-03394-5Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.1186/s13059-024-03394-5Direct OA link when available
- Concepts
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Interpretability, Indel, Benchmarking, Biology, Single-nucleotide polymorphism, Computational biology, Genetics, Phaser, Genome, 1000 Genomes Project, Structural variation, Data mining, Computer science, Artificial intelligence, Gene, Genotype, Engineering, Business, Marketing, Electrical engineeringTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
4Total citation count in OpenAlex
- Citations by year (recent)
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2025: 4Per-year citation counts (last 5 years)
- References (count)
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48Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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