BBCAnalyzer

BBCAnalyzer (Bases By CIGAR Analyzer) visualizes base counts from BAM alignment files to support evaluation and interpretation of variant calls in next-generation sequencing data.

Key Features:

• Visualization of Base Counts: Visualizes base counts at user-defined positions or regions in BAM files to assess expected mutations or regions of interest.
• Customizable Plots: Generates customizable plots integrating counted base numbers, reference bases, known mutations or polymorphisms, called mutations, and base quality metrics.
• Facilitation of Manual Inspection: Provides graphical summaries for inspecting common mutation sites, reducing manual inspection required when using standard variant callers.
• Independent Decision-Making: Enables users to assess variant presence independently of internal filters or allele frequency thresholds applied by variant calling software.

Scientific Applications:

• Clinical diagnostics: Supports precise variant calling and visual confirmation of expected mutations in clinical diagnostic workflows.
• Personalized medicine: Aids interpretation of hotspot mutations and other variants in personalized medicine analyses of next-generation sequencing data.

Methodology:

Extracts base counts from BAM files at user-defined positions or regions and synthesizes them with reference bases, known mutations/called variants, and base quality metrics to produce detailed plots.