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BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort

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dc.contributor.author김상우-
dc.date.accessioned2020-02-11T06:24:19Z-
dc.date.available2020-02-11T06:24:19Z-
dc.date.issued2019-
dc.identifier.issn1367-4803-
dc.identifier.urihttps://ir.ymlib.yonsei.ac.kr/handle/22282913/174661-
dc.description.abstractSUMMARY: 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 ∼100% accuracy in real WES, RNA-Seq and targeted sequencing data cohorts, even for small panels (<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. AVAILABILITY AND IMPLEMENTATION: BAMixChecker is available at https://github.com/heinc1010/BAMixChecker. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.-
dc.description.statementOfResponsibilityopen-
dc.languageEnglish-
dc.publisherOxford University Press-
dc.relation.isPartOfBIOINFORMATICS-
dc.rightsCC BY-NC-ND 2.0 KR-
dc.titleBAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort-
dc.typeArticle-
dc.contributor.collegeCollege of Medicine (의과대학)-
dc.contributor.departmentDept. of Biomedical Systems Informatics (의생명시스템정보학교실)-
dc.contributor.googleauthorHein Chun-
dc.contributor.googleauthorSangwoo Kim-
dc.identifier.doi10.1093/bioinformatics/btz479-
dc.contributor.localIdA00524-
dc.relation.journalcodeJ00299-
dc.identifier.eissn1367-4811-
dc.identifier.pmid31197312-
dc.contributor.alternativeNameKim, Sang Woo-
dc.contributor.affiliatedAuthor김상우-
dc.citation.volume35-
dc.citation.number22-
dc.citation.startPage4806-
dc.citation.endPage4808-
dc.identifier.bibliographicCitationBIOINFORMATICS, Vol.35(22) : 4806-4808, 2019-
dc.identifier.rimsid63538-
dc.type.rimsART-
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Biomedical Systems Informatics (의생명시스템정보학교실) > 1. Journal Papers

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