September 22, 2019  |  

A synthetic-diploid benchmark for accurate variant-calling evaluation.

Authors: Li, Heng and Bloom, Jonathan M and Farjoun, Yossi and Fleharty, Mark and Gauthier, Laura and Neale, Benjamin and MacArthur, Daniel

Existing benchmark datasets for use in evaluating variant-calling accuracy are constructed from a consensus of known short-variant callers, and they are thus biased toward easy regions that are accessible by these algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two fully homozygous human cell lines, which provides a relatively more accurate and less biased estimate of small-variant-calling error rates in a realistic context.

Journal: Nature methods
DOI: 10.1038/s41592-018-0054-7
Year: 2018

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