Agent-Skills.md

Agent Skills: Structural Variant Detector Skill

Structural variant detection skill for identifying CNVs, inversions, translocations, and complex rearrangements

bioinformaticsID: a5c-ai/babysitter/structural-variant-detector

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/structural-variant-detector

Skill Files

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/structural-variant-detector/SKILL.md

Skill Metadata

Name
structural-variant-detector
Description
Structural variant detection skill for identifying CNVs, inversions, translocations, and complex rearrangements

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)