DangerTrack: A scoring system to detect difficult-to-assess regions.

Area of Science:

• Genomics
• Bioinformatics
• Genetic Variation

Background:

• Structural variants and repetitive regions in genome assemblies significantly impact the accuracy of single nucleotide polymorphism (SNP) calling.
• Existing genome reference tracks do not adequately highlight regions prone to mapping and variant calling errors.

Purpose of the Study:

• To develop an intuitive visualization tool, DangerTrack, for identifying structural variant and repeat regions.
• To enhance the reliability of variant calling for clinical and research applications by flagging potentially erroneous calls.

Main Methods:

• Development of a novel genome track, DangerTrack, designed for visualization within existing genome browsers.
• Integration of DangerTrack with Genome Reference Consortium assembly tracks.

Main Results:

• DangerTrack effectively visualizes structural variant and repeat regions.
• The tool provides warnings for potentially miscalled variants, dubious quality calls, or regions with insertions/copy number expansions.

Conclusions:

• DangerTrack serves as a valuable resource for clinicians and researchers by highlighting areas of concern in variant calling.
• Careful examination of flagged regions, potentially including localized reassembly, is recommended for critical variant analysis.