Kronenberg, Z.
, Olson, N.
, Zook, J.
and Eberle, M.
(2024),
The Platinum Pedigree: A long-read benchmark for genetic variants, Nature Methods
(Accessed November 20, 2024)
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The Platinum Pedigree: A long-read benchmark for genetic variants
Published
Author(s)
Zev Kronenberg, , , Michael Eberle
Abstract
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance because existing standards often focus on specificity, neglecting completeness in difficult regions. To create a more comprehensive truth set, we used Mendelian inheritance in a large pedigree (CEPH-1463) to filter variants across Illumina, PacBio HiFi, and Oxford Nanopore platforms. This generated a variant map with over 4.7 million SNVs, 767,795 indels, 537,486 tandem repeats, and 24,315 structural variants, covering 2.77 Gb of the GRCh38 genome. This work adds 200 Mb of high-confidence regions, including 8% more small variants, and introduces the first tandem repeat and structural variant truth sets for NA12878. As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genotyping errors by 34%.Citation
Nature Methods
Pub Type
Journals
Keywords
bioinformatics, variant calling, benchmarking
Citation
Issues
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Created October 3, 2024, Updated October 29, 2024