| 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
- Calculate: Extract discordant read-pairs and split-reads.
- Execute: Build breakpoint graphs and candidate events.
- Assess: Perform read-depth and confidence filtering.
- Generate: Output structured VCF representation of SVs.
- 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 BAMvcf-ops — Downstream VCF merging logic
Citations
