PMID: 30013044DOI: 10.1038/s41592-018-0054-7Jul 18, 2018Paper
A synthetic-diploid benchmark for accurate variant-calling evaluation
Nature Methods
Heng LiDaniel MacArthur
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.
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Datasets Mentioned
BETA
NA12878
SRR2842672
SRR3099549
SRR2088062
SRR2088063
PRJEB13208
Methods Mentioned
BETA
PCR
Software Mentioned
Syndip
Samtools
Integrative Genomics Viewer ( IGV )
BWA
HC
PlatGen
RTG vcfeval
Platypus
MEM
FreeBayes
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