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bioRxiv · 10.1101/223297

New synthetic-diploid benchmark for accurate variant calling evaluation

Li, H.·Bloom, J. M.·Farjoun, Y.·Fleharty, M.·Gauthier, L. D.·Neale, B.·MacArthur, D.
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Abstract

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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Li, H., Bloom, J. M., Farjoun, Y., Fleharty, M., Gauthier, L. D., Neale, B., MacArthur, D.. 2017-11-22. New synthetic-diploid benchmark for accurate variant calling evaluation. https://doi.org/10.1101/223297

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