{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:21Z","timestamp":1740185121066,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T00:00:00Z","timestamp":1560470400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Korea Health Technology R&D Project","award":["HI14C1324"],"award-info":[{"award-number":["HI14C1324"]}]},{"DOI":"10.13039\/501100003710","name":"Korea Health Industry Development Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003710","name":"KHIDI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Health & Welfare, Republic of Korea"},{"name":"Bio & Medical Technology Development Program","award":["NRF-2016M3A9B6903439"],"award-info":[{"award-number":["NRF-2016M3A9B6903439"]}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007431","name":"NRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014188","name":"Ministry of Science and ICT","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Mislabeling in the process of next generation sequencing is a frequent problem that can cause an entire genomic analysis to fail, and a regular cohort-level checkup is needed to ensure that it has not occurred. We developed a new, automated tool (BAMixChecker) that accurately detects sample mismatches from a given BAM file cohort with minimal user intervention. BAMixChecker uses a flexible, data-specific set of single-nucleotide polymorphisms and detects orphan (unpaired) and swapped (mispaired) samples based on genotype-concordance score and entropy-based file name analysis. BAMixChecker shows \u223c100% accuracy in real WES, RNA-Seq and targeted sequencing data cohorts, even for small panels (&amp;lt;50 genes). BAMixChecker provides an HTML-style report that graphically outlines the sample matching status in tables and heatmaps, with which users can quickly inspect any mismatch events.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BAMixChecker is available at https:\/\/github.com\/heinc1010\/BAMixChecker<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz479","type":"journal-article","created":{"date-parts":[[2019,6,5]],"date-time":"2019-06-05T19:18:49Z","timestamp":1559762329000},"page":"4806-4808","source":"Crossref","is-referenced-by-count":7,"title":["BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort"],"prefix":"10.1093","volume":"35","author":[{"given":"Hein","family":"Chun","sequence":"first","affiliation":[{"name":"Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine , Seoul 03722, South Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5356-0827","authenticated-orcid":false,"given":"Sangwoo","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine , Seoul 03722, South Korea"}]}],"member":"286","published-online":{"date-parts":[[2019,6,14]]},"reference":[{"key":"2023013108355220500_btz479-B1","doi-asserted-by":"crossref","first-page":"3196","DOI":"10.1093\/bioinformatics\/btw389","article-title":"Conpair: concordance and contamination estimator for matched tumor-normal pairs","volume":"32","author":"Bergmann","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013108355220500_btz479-B2","doi-asserted-by":"crossref","first-page":"e103","DOI":"10.1093\/nar\/gkx193","article-title":"NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types","volume":"45","author":"Lee","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013108355220500_btz479-B6","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60 706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"2023013108355220500_btz479-B3","doi-asserted-by":"crossref","first-page":"300","DOI":"10.4143\/crt.2018.012","article-title":"Investigating the feasibility of targeted next-generation sequencing to guide the treatment of head and neck squamous cell carcinoma","volume":"51","author":"Lim","year":"2019","journal-title":"Cancer Res Treat"},{"key":"2023013108355220500_btz479-B4","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/bioinformatics\/btw239","article-title":"BAM-matcher: a tool for rapid NGS sample matching","volume":"32","author":"Wang","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013108355220500_btz479-B5","doi-asserted-by":"crossref","first-page":"2104","DOI":"10.1093\/bioinformatics\/btr323","article-title":"MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic 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