title: BBCAnalyzer: a visual approach to facilitate variant calling.
abstract: BACKGROUND
  Deriving valid variant calling results from raw next-generation sequencing data is a particularly challenging task, especially with respect to clinical diagnostics and personalized medicine. However, when using classic variant calling software, the user usually obtains nothing more than a list of variants that pass the corresponding caller's internal filters. Any expected mutations (e.g. hotspot mutations), that have not been called by the software, need to be investigated manually.
  
  
  RESULTS
  BBCAnalyzer (Bases By CIGAR Analyzer) provides a novel visual approach to facilitate this step of time-consuming, manual inspection of common mutation sites. BBCAnalyzer is able to visualize base counts at predefined positions or regions in any sequence alignment data that are available as BAM files. Thereby, the tool provides a straightforward solution for evaluating any list of expected mutations like hotspot mutations, or even whole regions of interest. In addition to an ordinary textual report, BBCAnalyzer reports highly customizable plots. Information on the counted number of bases, the reference bases, known mutations or polymorphisms, called mutations and base qualities is summarized in a single plot. By uniting this information in a graphical way, the user may easily decide on a variant being present or not - completely independent of any internal filters or frequency thresholds.
  
  
  CONCLUSIONS
  BBCAnalyzer provides a unique, novel approach to facilitate variant calling where classical tools frequently fail to call. The R package is freely available at http://bioconductor.org . The local web application is available at Additional file 2. A documentation of the R package (Additional file 1) as well as the web application (Additional file 2) with detailed descriptions, examples of all input- and output elements, exemplary code as well as exemplary data are included. A video demonstrates the exemplary usage of the local web application (Additional file 3). Additional file 3: Supplement_3. Video demonstrating the exemplary usage of the web application "BBCAnalyzer". (MP4 11571 kb).
authors.affiliation: Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Münster, 48149, Germany. sarah.sandmann@uni-muenster.de.
authors.forename: Sarah
authors.identifier: http://orcid.org/0000-0002-5011-0641
authors.initials: S
authors.lastname: Sandmann
authors.affiliation: Laboratory Hematology, RadboudUMC, Geert Grooteplein zuid 8, Nijmegen, 6525, Netherlands.
authors.forename: Aniek O
authors.initials: AO
authors.lastname: de Graaf
authors.affiliation: Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Münster, 48149, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Dugas
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation; D016415:Sequence Alignment; D012984:Software
keywords: Hotspot mutations; Next-generation sequencing; Personalized medicine; Variant calling; Visualization