Evidence map›Paper›PMID 41894165›Full record

ArticleBriefings in bioinformatics2026

Comparison of variant callers using 60 532 multi-ancestry whole genome sequences.

Hufeng Zhou, Zilin Li, Derek Shyr, Xihao Li, Haoyu Yang, Rounak Dey, Yushi Tang, Robert Maier, Eric Boerwinkle, Steve Buyske and 15 more

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Briefings in bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Hufeng ZhouDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, United States.ORCID 0000-0001-9382-5674
Zilin LiDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, United States.
Derek ShyrDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, United States.
Xihao LiDepartment of Biostatistics, University of North Carolina at Chapel Hill, 3101 McGavran-Greenberg Hall, 135 Dauer Drive, Chapel Hill, NC 27599, United States.
Haoyu YangDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, United States.
Rounak DeyDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, United States.
Yushi TangLewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA.
Robert MaierMassachusetts General Hospital, Analytic and Translational Genetics Unit, 185 Cambridge Street, Boston, MA 02114, United States.
Eric BoerwinkleSchool of Public Health, University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, United States.
Steve BuyskeDepartment of Statistics, Rutgers, The State University of New Jersey, 110 Frelinghuysen Road, Piscataway, NJ 08854, United States.
Mark DalyMassachusetts General Hospital, Analytic and Translational Genetics Unit, 185 Cambridge Street, Boston, MA 02114, United States.
Adam FelsenfeldNational Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, United States.
Richard A GibbsDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States.
Namrata GuptaMassachusetts General Hospital, Analytic and Translational Genetics Unit, 185 Cambridge Street, Boston, MA 02114, United States.
Ira M HallCenter for Genomic Health, Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, United States.
Tara MatiseDepartment of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, United States.
Ginger A MetcalfDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States.
Albert SmithDepartment of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States.
Catherine ReevesNew York Genome Center, 101 Avenue of the Americas, New York, NY 10013, United States.
Heidi J SofiaNational Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, United States.
Nathan O StitzielDepartment of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, United States.
Michael C ZodyNew York Genome Center, 101 Avenue of the Americas, New York, NY 10013, United States.
NHGRI Genome Sequencing Program (GSP) Consortium
Benjamin NealeMassachusetts General Hospital, Analytic and Translational Genetics Unit, 185 Cambridge Street, Boston, MA 02114, United States.
Xihong LinDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, United States.ORCID 0000-0001-7067-7752

Funding

Center for Common Disease GeneticsUM1HG008895 · NHGRI · BROAD INSTITUTE, INC. · PI DALY, MARK JOSEPH, GABRIEL, STACEY · 2016 to 2020
$111.2M
Genomic Architecture of Common Disease in Diverse Populations: WGS of Ongoing Hemorrhagic Stroke Study SupplementUM1HG008898 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2016 to 2020
$77.0M
Supplement Proposal: Accelerated Genome Aggregation and Joint Variant Calling EffortUM1HG008853 · NHGRI · WASHINGTON UNIVERSITY · PI HALL, IRA M, MILBRANDT, JEFFREY D · 2016 to 2020
$76.2M
New York Center for Collaborative Research In Common Disease Genomics: Genome Aggregation and Joint Variant Calling for CCDG Freeze2UM1HG008901 · NHGRI · NEW YORK GENOME CENTER · PI MANIATIS, THOMAS P, WIGLER, MICHAEL H · 2016 to 2020
$56.6M
Powering whole genome sequence-based genetic discovery for common human diseases- Extended 2021-2022.U01HG009088 · NHGRI · HARVARD SCHOOL OF PUBLIC HEALTH · PI LIN, XIHONG, NEALE, BENJAMIN MICHAEL · 2016 to 2021
$5.1M
NHGRI Genome Sequencing Program Coordinating CenterU24HG008956 · NHGRI · RUTGERS, THE STATE UNIV OF N.J. · PI BUYSKE, STEVEN G, MATISE, TARA C. · 2016 to 2020
$4.9M
NHGRI NIH HHS U01 HG009088NHGRI NIH HHS U24 HG008956NHGRI NIH HHS UM1 HG008853NHGRI NIH HHS UM1 HG008895NHGRI NIH HHS UM1 HG008898NHGRI NIH HHS UM1 HG008901NHLBI NIH HHS R01-HL163560
6 · The paper itself

Abstract

Whole genome sequencing (WGS) studies play a pivotal role in studying the genetic underpinnings of human diseases and traits. High quality and reproducible variant calling is the cornerstone for the success of downstream analyses, including WGS association studies and polygenic risk prediction. This paper compares the data quality, performance, and concordance of two widely used WGS variant callers, the Genome Analysis Toolkit (GATK) and Variant Tool set that discovers short variants (VT), using 60 532 multi-ancestry whole genomes sequenced by the Centers for Common Disease Genomics (CCDGs) of the NHGRI Genome Sequencing Program. Our findings show that both QCed GATK and VT pipelines yield highly consistent and reliable called Single Nucleotide Variants (SNVs) in large-scale WGS studies, supporting their agreements in joint variants calling. However, the two pipelines exhibit greater discrepancies in calling insertions and deletions (INDELs).

Indexed as

Genetic VariationGenome, HumanPolymorphism, Single NucleotideSoftwareWhole Genome SequencingGenome-Wide Association StudyGenomicsHumanscomparisongeneticsquality controlvariant callingwhole genome sequencing

Identifiers

PMID41894165
PMCPMC13023369

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.