Dunn, T.
, Zook, J.
, Holt, J.
and Narayanasamy, S.
(2024),
Jointly benchmarking small and structural variant calls with vcfdist, Genome Biology, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=957429
(Accessed October 9, 2025)
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Jointly benchmarking small and structural variant calls with vcfdist
Published
Author(s)
Tim Dunn, , James Holt, Satish Narayanasamy
Abstract
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.Citation
Genome Biology
Volume
25
Pub Type
Journals
Download Paper
Keywords
human genome, variant calling, benchmarking, structural variants
Citation
Issues
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Created October 2, 2024, Updated March 4, 2025