Cited 4 times in
BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort
DC Field | Value | Language |
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dc.contributor.author | 김상우 | - |
dc.date.accessioned | 2020-02-11T06:24:19Z | - |
dc.date.available | 2020-02-11T06:24:19Z | - |
dc.date.issued | 2019 | - |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | https://ir.ymlib.yonsei.ac.kr/handle/22282913/174661 | - |
dc.description.abstract | SUMMARY: 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.statementOfResponsibility | open | - |
dc.language | English | - |
dc.publisher | Oxford University Press | - |
dc.relation.isPartOf | BIOINFORMATICS | - |
dc.rights | CC BY-NC-ND 2.0 KR | - |
dc.title | BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort | - |
dc.type | Article | - |
dc.contributor.college | College of Medicine (의과대학) | - |
dc.contributor.department | Dept. of Biomedical Systems Informatics (의생명시스템정보학교실) | - |
dc.contributor.googleauthor | Hein Chun | - |
dc.contributor.googleauthor | Sangwoo Kim | - |
dc.identifier.doi | 10.1093/bioinformatics/btz479 | - |
dc.contributor.localId | A00524 | - |
dc.relation.journalcode | J00299 | - |
dc.identifier.eissn | 1367-4811 | - |
dc.identifier.pmid | 31197312 | - |
dc.contributor.alternativeName | Kim, Sang Woo | - |
dc.contributor.affiliatedAuthor | 김상우 | - |
dc.citation.volume | 35 | - |
dc.citation.number | 22 | - |
dc.citation.startPage | 4806 | - |
dc.citation.endPage | 4808 | - |
dc.identifier.bibliographicCitation | BIOINFORMATICS, Vol.35(22) : 4806-4808, 2019 | - |
dc.identifier.rimsid | 63538 | - |
dc.type.rims | ART | - |
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