A synthetic-diploid benchmark for accurate variant-calling evaluation.
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ABSTRACT:
SUBMITTER: Li H
PROVIDER: S-EPMC6341484 | biostudies-literature | 2018 Aug
REPOSITORIES: biostudies-literature
Publications
A synthetic-diploid benchmark for accurate variant-calling evaluation.
Li Heng H Bloom Jonathan M JM Farjoun Yossi Y Fleharty Mark M Gauthier Laura L Neale Benjamin B MacArthur Daniel D
Nature methods 20180716 8
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. ...[more]
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