structural-variant-detector

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"]}

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)