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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Citations

Jul 12, 2018·Bioinformatics·James K BonfieldRichard Durbin
Mar 22, 2019·Genome Research·Patrick MarksDeanna M Church
Apr 4, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Prachi KothiyalJohn E Niederhuber
May 17, 2019·Genetics, Selection, Evolution : GSE·Danang CrysnantoHubert Pausch
May 18, 2019·Bioinformatics·Daniel TelloJorge Duitama
Apr 23, 2020·Bioinformatics·Charlotte A DarbyBen Langmead
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Aug 14, 2019·Nature Biotechnology·Aaron M WengerMichael W Hunkapiller
Apr 3, 2019·Nature Biotechnology·Justin M ZookMarc Salit
Aug 10, 2019·Molecular Biology and Evolution·Lorenzo TattiniGianni Liti
Jun 4, 2020·Genome Biology·Alaina ShumateSteven L Salzberg
Sep 24, 2020·Nature Communications·Chen-Shan ChinJustin M Zook
Aug 14, 2020·The New England Journal of Medicine·Kate E StanleyDavid B Goldstein
May 29, 2020·Nature·Konrad J KarczewskiDaniel G MacArthur
Nov 30, 2019·Nature Communications·Hannes P EggertssonPall Melsted
Sep 15, 2020·EMBO Molecular Medicine·Christian BruefferLao H Saal
Dec 9, 2020·Nature Biotechnology·Shilpa GargHeng Li
Dec 22, 2020·Bioinformatics·David Heller, Martin Vingron
Feb 13, 2021·NAR Genomics and Bioinformatics·Wouter De CosterPeter De Rijk
Oct 28, 2020·Genome Medicine·Daniel C Koboldt
Feb 21, 2021·Genome Biology·Stephan Schmeing, Mark D Robinson
Mar 15, 2021·Human Mutation·Lauris KaplinskiMaido Remm
Mar 31, 2021·Nature Biotechnology·Daniel P CookeGerton Lunter
May 30, 2021·Nature Reviews. Genetics·Wouter De CosterFritz J Sedlazeck
May 18, 2021·Genetic Epidemiology·Anthony F HerzigEmmanuelle Génin
Oct 9, 2021·Bioinformatics·Heng Li
Feb 1, 2022·Nucleic Acids Research·Kez Cleal, Duncan M Baird
Dec 31, 2021·Genome Research·Daniel P CookeGerton Lunter

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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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