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New synthetic-diploid benchmark for accurate variant calling evaluation

By Heng Li, Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura Gauthier, Benjamin M. Neale, Daniel G. MacArthur

Posted 22 Nov 2017
bioRxiv DOI: 10.1101/223297 (published DOI: 10.1038/s41592-018-0054-7)

Constructed from the consensus of multiple variant callers based on short-read data, existing benchmark datasets for evaluating variant calling accuracy are biased toward easy regions accessible by known algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two human cell lines that are homozygous across the whole genome. This benchmark provides a more accurate and less biased estimate of the error rate of small variant calls in a realistic context.

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