A synthetic-diploid benchmark for accurate variant-calling evaluation

被引：129

作者：

Li, Heng ^{[1
]}

Bloom, Jonathan M. ^{[1
]}

Farjoun, Yossi ^{[1
]}

Fleharty, Mark ^{[1
]}

Gauthier, Laura ^{[1
]}

Neale, Benjamin ^{[1
,2
]}

MacArthur, Daniel ^{[1
,2
]}

机构：

[1] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

[2] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA

来源：

NATURE METHODS | 2018年 / 15卷 / 08期

基金：

美国国家卫生研究院;

关键词：

GENOME ASSEMBLIES; DISCOVERY; FRAMEWORK; SNP;

D O I：

10.1038/s41592-018-0054-7

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：595 / +

页数：6

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