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

TitleA synthetic-diploid benchmark for accurate variant-calling evaluation.
Publication TypeJournal Article
Year of Publication2018
AuthorsLi, H, Bloom, JM, Farjoun, Y, Fleharty, M, Gauthier, L, Neale, B, MacArthur, D
JournalNat Methods
Volume15
Issue8
Pagination595-597
Date Published2018 Aug
ISSN1548-7105
Abstract

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.

DOI10.1038/s41592-018-0054-7
Alternate JournalNat. Methods
PubMed ID30013044
PubMed Central IDPMC6341484
Grant ListR01 HG010040 / HG / NHGRI NIH HHS / United States
U01 HG009088 / HG / NHGRI NIH HHS / United States
U54 DK105566 / DK / NIDDK NIH HHS / United States