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name: structural-variant-detector description: Structural variant detection skill for identifying CNVs, inversions, translocations, and complex rearrangements allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • variant-analysis
  • structural-variants
  • cnv
  • sv graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:graph-algorithms, skill-area:statistical-analysis, skill-area:data-analysis] workflows: [workflow:experiment-design] roles: [role:research-engineer, role:biomedical-engineer]

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Structural Variant Detector Skill

Purpose

Enable structural variant detection for identifying CNVs, inversions, translocations, and complex rearrangements.

Capabilities

• Split-read and paired-end SV calling
• Copy number variation detection
• Mobile element insertion detection
• Complex SV resolution
• SV annotation and visualization
• Multi-caller integration

Usage Guidelines

• Use multiple callers for comprehensive detection
• Integrate results from different algorithms
• Validate SVs with independent methods
• Annotate SVs with functional impact
• Visualize SVs for manual review
• Document caller combinations and filters

Dependencies

• Manta
• DELLY
• CNVkit
• LUMPY
• GRIDSS

Process Integration

• Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
• Tumor Molecular Profiling (tumor-molecular-profiling)
• Long-Read Sequencing Analysis (long-read-analysis)