{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T16:03:24Z","timestamp":1774627404969,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T00:00:00Z","timestamp":1774569600000},"content-version":"vor","delay-in-days":26,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000050","name":"NHLBI","doi-asserted-by":"publisher","award":["R01-HL163560"],"award-info":[{"award-number":["R01-HL163560"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NHGRI Genome Sequencing Program (GSP) Coordinating Center grant to Rutgers","award":["U24 HG008956"],"award-info":[{"award-number":["U24 HG008956"]}]},{"DOI":"10.13039\/100016149","name":"New York Genome Center","doi-asserted-by":"publisher","award":["UM1 HG008901"],"award-info":[{"award-number":["UM1 HG008901"]}],"id":[{"id":"10.13039\/100016149","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007915","name":"Baylor College of Medicine","doi-asserted-by":"publisher","award":["UM1 HG008898"],"award-info":[{"award-number":["UM1 HG008898"]}],"id":[{"id":"10.13039\/100007915","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013114","name":"Broad Institute of MIT and Harvard","doi-asserted-by":"publisher","award":["UM1 HG008895"],"award-info":[{"award-number":["UM1 HG008895"]}],"id":[{"id":"10.13039\/100013114","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CCDG awards to Washington University in St. Louis","award":["UM1 HG008853"],"award-info":[{"award-number":["UM1 HG008853"]}]},{"name":"NHGRI GSP Analysis Center award to Harvard University","award":["U01 HG009088"],"award-info":[{"award-number":["U01 HG009088"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u00a0532 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).<\/jats:p>","DOI":"10.1093\/bib\/bbag130","type":"journal-article","created":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T15:06:02Z","timestamp":1774623962000},"source":"Crossref","is-referenced-by-count":0,"title":["Comparison of variant callers using 60\u00a0532 multi-ancestry whole genome sequences"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9382-5674","authenticated-orcid":false,"given":"Hufeng","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , 677 Huntington Avenue, Boston, MA 02115 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zilin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. 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, 1200 Pressler Street, Houston, TX 77030 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steve","family":"Buyske","sequence":"additional","affiliation":[{"name":"Department of Statistics, Rutgers, The State University of New Jersey , 110 Frelinghuysen Road, Piscataway, NJ 08854 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Daly","sequence":"additional","affiliation":[{"name":"Massachusetts General Hospital, Analytic and Translational Genetics Unit , 185 Cambridge Street, Boston, MA 02114 ,","place":["United States"]},{"name":"Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard , 75 Ames Street, Cambridge, MA 02142 ,","place":["United States"]},{"name":"Program in Medical and Population Genetics, Broad Institute of Harvard and MIT , 415 Main Street, Cambridge, MA 02142 ,","place":["United 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States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ira M","family":"Hall","sequence":"additional","affiliation":[{"name":"Center for Genomic Health, Department of Genetics, Yale School of Medicine , 333 Cedar Street, New Haven, CT 06510 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tara","family":"Matise","sequence":"additional","affiliation":[{"name":"Department of Genetics, Rutgers University , 145 Bevier Road, Piscataway, NJ 08854 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ginger A","family":"Metcalf","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Albert","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of 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