title: Repeat- and error-aware comparison of deletions.
abstract: BACKGROUND
  The number of reported genetic variants is rapidly growing, empowered by ever faster accumulation of next-generation sequencing data. A major issue is comparability. Standards that address the combined problem of inaccurately predicted breakpoints and repeat-induced ambiguities are missing. This decisively lowers the quality of 'consensus' callsets and hampers the removal of duplicate entries in variant databases, which can have deleterious effects in downstream analyses.
  
  
  RESULTS
  We introduce a sound framework for comparison of deletions that captures both tool-induced inaccuracies and repeat-induced ambiguities. We present a maximum matching algorithm that outputs virtual duplicates among two sets of predictions/annotations. We demonstrate that our approach is clearly superior over ad hoc criteria, like overlap, and that it can reduce the redundancy among callsets substantially. We also identify large amounts of duplicate entries in the Database of Genomic Variants, which points out the immediate relevance of our approach.
  
  
  METHODS
  Implementation is open source and available from https://bitbucket.org/readdi/readdi
  
  
  BACKGROUND
  roland.wittler@uni-bielefeld.de or t.marschall@mpi-inf.mpg.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany, Center for Bioinformatics, Saarland University and Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany, Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Amsterdam, The Netherlands and Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland.
authors.forename: Roland
authors.initials: R
authors.lastname: Wittler
authors.affiliation: Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany, Center for Bioinformatics, Saarland University and Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany, Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Amsterdam, The Netherlands and Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland.
authors.forename: Tobias
authors.initials: T
authors.lastname: Marschall
authors.affiliation: Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany, Center for Bioinformatics, Saarland University and Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany, Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Amsterdam, The Netherlands and Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schönhuth
authors.affiliation: Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany, Center for Bioinformatics, Saarland University and Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany, Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Amsterdam, The Netherlands and Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland.
authors.forename: Veli
authors.initials: V
authors.lastname: Mäkinen
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D014644:Genetic Variation / Q000235:genetics*; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008962:Models, Theoretical; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000592:standards*; D017384:Sequence Deletion / Q000235:genetics*; D012984:Software