genomics-sv-detection

genomics-sv-detection

When to use

The user has an SV VCF (from Manta, Delly, Lumpy, Sniffles, etc.) and wants per-type counts (DEL / DUP / INV / TRA / INS), size classification (small 50 bp–1 kb / medium 1 kb–100 kb / large 100 kb–10 Mb / very-large > 10 Mb), and BND breakend resolution.

The script does NOT call SVs from a BAM. Run an external SV caller first; this skill summarises its VCF output.

Inputs & Outputs

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Inputs

• File types: .vcf

Outputs

• tables/structural_variants.csv
• report.md
• result.json

Flow

1. Load VCF (--input <sv.vcf>) or generate a demo SV VCF at output_dir/demo_structural_variants.vcf with --n-svs records (sv_detection.py:170).
2. Parse records; read INFO/SVTYPE (sv_detection.py:103). Records without INFO/SVTYPE (e.g. pure BND ALT notation from Manta) classify as UNKNOWN — there is NO BND-to-TRA resolution.
3. Compute abs(SVLEN) for size classification (sv_detection.py:105); bin into size classes; aggregate per-type counts.
4. Write tables/structural_variants.csv (sv_detection.py:343) + report.md + result.json (:346).

Gotchas

• No SV caller is invoked. This skill ingests an SV VCF — it does NOT run Manta / Delly / Lumpy / Sniffles. To CALL SVs, run an external pipeline first.
• --input REQUIRED unless --demo. sv_detection.py:330 raises ValueError("--input required when not using --demo"); non-existent paths raise FileNotFoundError at :333.
• --n-svs only affects --demo (sv_detection.py:319, default 100). Silently ignored when --input is set.
• Pure BND records without INFO/SVTYPE classify as UNKNOWN. sv_detection.py:103 reads only INFO/SVTYPE; there is no BND ALT-notation parser and no MATEID pairing logic. Manta callsets that emit translocations as paired BND records (without an SVTYPE=TRA INFO field) will appear as UNKNOWN, not TRA. Pre-process with bcftools view -i 'INFO/SVTYPE!=""' or with a Manta-specific BND→TRA resolver upstream.
• SVLEN is stored as absolute value in the CSV. sv_detection.py:105 writes abs(int(info.get("SVLEN", end - pos))) — a 1234-bp deletion becomes 1234 in the CSV regardless of the input sign. The original signed SVLEN is NOT preserved.
• Demo VCF mixes DEL / DUP / INV / TRA at fixed proportions. Useful for orchestrator smoke tests; not biologically meaningful.

Key CLI

# Demo (100 synthetic SVs)
python omicsclaw.py run genomics-sv-detection --demo --output /tmp/sv_demo

# Custom demo size
python omicsclaw.py run genomics-sv-detection --demo --n-svs 500 \
  --output /tmp/sv_demo_large

# Real SV VCF
python omicsclaw.py run genomics-sv-detection \
  --input manta_diploid.vcf --output results/

See also

• references/parameters.md — every CLI flag
• references/methodology.md — SVTYPE / BND semantics, size-class boundaries
• references/output_contract.md — tables/structural_variants.csv schema
• Adjacent skills: genomics-alignment (upstream — provides BAMs for SV callers), genomics-variant-calling (parallel — small SNVs / indels), genomics-cnv-calling (parallel — copy-number from depth, complementary to SV callers), genomics-variant-annotation (downstream — functional impact of breakpoints)