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A synthetic-diploid benchmark for accurate variant-calling evaluation
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The calls in the HG002 truth set were based on aligning a high-confidence assembly using dipcall.
“The calls in this set were based on aligning a high-confidence assembly using dipcall 53 (labeled in figure as 'dipcall CHM13 v2.0').”
From Pangenome graph construction from genome alignments with Minigraph-Cactus (2024) · cites this paper as [53]
The Methods section (‘Constructing the truth call set and confident regions’; page not provided) supports the general idea of deriving variant calls by aligning assemblies to a reference. But it describes CHM1 and CHM13 assemblies aligned with minimap2 to construct the Syndip call set, not an HG002 truth set generated using dipcall or CHM13 v2.0. (LLM, conf=0.86)
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Metadata
- Authors
- Li, H., Bloom, J. M., Farjoun, Y., Fleharty, M., Gauthier, L., Neale, B., & MacArthur, D.
- Venue
- Nature Methods
- Published
- 2018-07-16
- Volume
- 15
- Issue
- 8
- Pages
- 595-597
- ISSN
- 1548-7091
- 1548-7105
- PMC
- PMC6341484
- Cited by
- 253
- References
- 4
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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