title: Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.
abstract: BACKGROUND
  The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map.
  
  
  RESULTS
  Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant.
  
  
  BACKGROUND
  SplazerS is available from http://www.seqan.de/projects/ splazers.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, Freie Universität Berlin, Takustrasse 9, Max-Planck-Institute for Molecular Genetics, Berlin, Germany. emde@inf.fu-berlin.de
authors.forename: Anne-Katrin
authors.initials: AK
authors.lastname: Emde
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.forename: David
authors.initials: D
authors.lastname: Weese
authors.forename: Ruping
authors.initials: R
authors.lastname: Sun
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
authors.forename: Vera M
authors.initials: VM
authors.lastname: Kalscheuer
authors.forename: Stefan A
authors.initials: SA
authors.lastname: Haas
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
mesh_terms: D000465:Algorithms; D023281:Genomics / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D017422:Sequence Analysis, DNA