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

Authors
 Hein Chun  ;  Sangwoo Kim 
Citation
 BIOINFORMATICS, Vol.35(22) : 4806-4808, 2019 
Journal Title
 BIOINFORMATICS 
ISSN
 1367-4803 
Issue Date
2019
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.
Files in This Item:
T201905216.pdf Download
DOI
10.1093/bioinformatics/btz479
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Biomedical Systems Informatics (의생명시스템정보학교실) > 1. Journal Papers
Yonsei Authors
Kim, Sangwoo(김상우) ORCID logo https://orcid.org/0000-0001-5356-0827
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/174661
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