%0 Journal Article %J Nat Methods %D 2018 %T A synthetic-diploid benchmark for accurate variant-calling evaluation. %A Li, Heng %A Bloom, Jonathan M %A Farjoun, Yossi %A Fleharty, Mark %A Gauthier, Laura %A Neale, Benjamin %A MacArthur, Daniel %K Algorithms %K Benchmarking %K Cell Line, Tumor %K Databases, Genetic %K Diploidy %K Female %K Genetic Variation %K Genome, Human %K Homozygote %K Humans %K Hydatidiform Mole %K Pregnancy %K Synthetic Biology %K Uterine Neoplasms %K Whole Genome Sequencing %X

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.

%B Nat Methods %V 15 %P 595-597 %8 2018 08 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/30013044?dopt=Abstract %R 10.1038/s41592-018-0054-7