# Structural Variant Detector

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

- Skill: `a5c-ai/structural-variant-detector` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/structural-variant-detector`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/structural-variant-detector/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/structural-variant-detector

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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)