title: Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination.
abstract: Advances in sequencing technologies have remarkably lowered the detection limit of somatic variants to a low frequency. However, calling mutations at this range is still confounded by many factors including environmental contamination. Vector contamination is a continuously occurring issue and is especially problematic since vector inserts are hardly distinguishable from the sample sequences. Such inserts, which may harbor polymorphisms and engineered functional mutations, can result in calling false variants at corresponding sites. Numerous vector-screening methods have been developed, but none could handle contamination from inserts because they are focusing on vector backbone sequences alone.
  
  
  
  We developed a novel method-Vecuum-that identifies vector-originated reads and resultant false variants. Since vector inserts are generally constructed from intron-less cDNAs, Vecuum identifies vector-originated reads by inspecting the clipping patterns at exon junctions. False variant calls are further detected based on the biased distribution of mutant alleles to vector-originated reads. Tests on simulated and spike-in experimental data validated that Vecuum could detect 93% of vector contaminants and could remove up to 87% of variant-like false calls with 100% precision. Application to public sequence datasets demonstrated the utility of Vecuum in detecting false variants resulting from various types of external contamination.
  
  
  
  Java-based implementation of the method is available at http://vecuum.sourceforge.net/ CONTACT: swkim@yuhs.acSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea.
authors.forename: Junho
authors.initials: J
authors.lastname: Kim
authors.affiliation: Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea.
authors.forename: Ju Heon
authors.initials: JH
authors.lastname: Maeng
authors.affiliation: Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, South Korea.
authors.forename: Jae Seok
authors.initials: JS
authors.lastname: Lim
authors.affiliation: Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea.
authors.forename: Hyeonju
authors.initials: H
authors.lastname: Son
authors.affiliation: Department of Convergence Technology Research, Korea Institute of Science and Technology Information, Daejeon 34141, South Korea.
authors.forename: Junehawk
authors.initials: J
authors.lastname: Lee
authors.affiliation: Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, South Korea.
authors.forename: Jeong Ho
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea.
authors.forename: Sangwoo
authors.initials: S
authors.lastname: Kim
mesh_terms: D000483:Alleles; D005822:Genetic Vectors; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D011995:Recombination, Genetic; D012984:Software