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).