DangerTrack

DangerTrack identifies genomic regions containing structural variants and repetitive sequences that compromise read mapping and variant calling accuracy.

Key Features:

• Scoring system: Generates scores that highlight regions with potential mapping or calling difficulties due to structural variants and repetitive sequences.
• Genome Reference Consortium integration: Integrates as a track alongside Genome Reference Consortium assembly tracks for comparative assessment of regions of interest.
• Dubious-call warning system: Flags variants that may be incorrectly called or of dubious quality, including insertions and copy number expansions.
• Localized reassembly facilitation: Identifies regions that warrant localized reassembly and more detailed examination to improve calling accuracy.

Scientific Applications:

• Clinical diagnostics: Flags regions where structural variants or repeats may produce unreliable SNP or other variant calls that could affect clinical interpretation.
• Research investigations: Identifies problematic genomic regions for downstream analyses, variant curation, and assembly evaluation.
• Personalized medicine support: Guides targeted reanalysis and localized reassembly to improve variant reliability for individual genetic assessments.

Methodology:

Implements a genomic track and scoring system that highlights structural variant and repeat regions and integrates with Genome Reference Consortium assembly tracks to flag variants of dubious quality and indicate loci for potential localized reassembly.