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BBCAnalyzer: a visual approach to facilitate variant calling.

Sarah Sandmann1, Aniek O de Graaf2, Martin Dugas3

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BMC Bioinformatics
|March 1, 2017
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Summary

BBCAnalyzer offers a visual approach to improve variant calling from next-generation sequencing data. This tool aids in manually inspecting mutations, especially when standard software filters are insufficient.

Keywords:
Hotspot mutationsNext-generation sequencingPersonalized medicineVariant callingVisualization

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate variant calling from next-generation sequencing (NGS) data is crucial for clinical diagnostics and personalized medicine.
  • Traditional variant callers often output only filtered variants, necessitating manual investigation of uncalled mutations.
  • Identifying expected mutations, such as hotspot mutations, requires time-consuming manual inspection of sequencing data.

Purpose of the Study:

  • To introduce BBCAnalyzer (Bases By CIGAR Analyzer), a novel tool for visual inspection of variant calling results.
  • To facilitate the manual review of potential mutations missed by automated variant callers.
  • To provide a user-friendly solution for evaluating specific mutation sites or regions of interest in sequencing data.

Main Methods:

  • BBCAnalyzer visualizes base counts at specified positions or regions within sequence alignment data (BAM files).
  • The tool integrates information on base counts, reference bases, known variants, called mutations, and base qualities into customizable plots.
  • It offers both textual reports and graphical summaries for variant evaluation.

Main Results:

  • BBCAnalyzer enables straightforward assessment of expected mutations, including hotspot mutations.
  • The tool allows users to independently evaluate variants without relying on internal filters or frequency thresholds.
  • Customizable plots provide a consolidated view of critical variant information, aiding in decision-making.

Conclusions:

  • BBCAnalyzer presents a unique visual method to enhance variant calling, addressing limitations of classical tools.
  • The software is available as a free R package on Bioconductor and includes comprehensive documentation and examples.
  • A local web application with a demonstration video is also provided for user guidance.