genomics-sv-detection

name	genomics-sv-detection
description	Structural variant detection (DEL/DUP/INV/TRA): SV VCF parsing with BND notation, size classification (50bp-10Mb), evidence types. Wraps Manta, Lumpy, Delly, Sniffles.
version	0.2.0
author	OmicsClaw
license	MIT
tags	["genomics","structural-variants","Manta","Delly","Sniffles"]
metadata	{"omicsclaw":{"domain":"genomics","emoji":"🧱","trigger_keywords":["structural variant","SV","Manta","Delly","Lumpy","Sniffles"],"allowed_extra_flags":["--method"],"legacy_aliases":["sv-detect"],"saves_h5ad":false}}

🧱 Structural Variant Detection

Structural variant calling for deletions, duplications, inversions, and translocations. Wraps Manta, Lumpy, Delly, Sniffles.

CLI Reference

python omicsclaw.py run genomics-sv-detection --demo
python omicsclaw.py run genomics-sv-detection --input <data.bam> --output <dir>

Why This Exists

• Without it: Conventional SNV callers miss massive >50bp translocations, inversions, or large deletions
• With it: Split-reads and paired-end discordance are utilized to find complex structural variation
• Why OmicsClaw: Encapsulates multiple specialized SV tools (Manta, Delly) with unified orchestration

Workflow

1. Calculate: Extract discordant read-pairs and split-reads.
2. Execute: Build breakpoint graphs and candidate events.
3. Assess: Perform read-depth and confidence filtering.
4. Generate: Output structured VCF representation of SVs.
5. Report: Tabulate key SV counts.

Example Queries

• "Call structural variants using Manta"
• "Detect chromosomal inversions using Sniffles from long reads"

Output Structure

output_directory/
├── report.md
├── result.json
├── variants_sv.vcf.gz
├── figures/
│   └── sv_length_distribution.png
├── tables/
│   └── sv_summary.csv
└── reproducibility/
    ├── commands.sh
    ├── requirements.txt
    └── checksums.sha256

Safety

• Local-first: Strict offline processing without external upload.
• Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
• Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

• align — Upstream generation of BAM
• vcf-ops — Downstream VCF merging logic

Citations

• Manta
• Delly
• Sniffles