agentmods.dev

genomics-sv-detection

genomics-sv-detection is a skill for Claude Code, Codex from TianGzlab/OmicsClaw. It costs 78 tokens per session (1,155 once invoked), scanned A, original, Apache-2.0.

A tool for summarising structural variants in a VCF file, a standard text format for genetic differences. Structural variants are large DNA changes such as deletions, duplications, inversions, and rearrangements.

In plain words
What is it for?
Use it with an SV VCF produced by callers such as Manta, Delly, Lumpy, or Sniffles to create CSV tables, a report, and JSON results.
Why use it?
It organises existing variant-calling results by type and size instead of requiring manual VCF inspection. It does not discover variants from sequencing data.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 160repo +1 1mo ago A scan SkillSpector: warn 78 tokens original Apache-2.0

Good fit Use it with an SV VCF produced by callers such as Manta, Delly, Lumpy, or Sniffles to create CSV tables, a report, and JSON results.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/tiangzlab/omicsclaw/genomics-sv-detection
View source ↗ TianGzlab/OmicsClaw tiangzlab.github.io
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add TianGzlab/OmicsClaw --skill genomics-sv-detection
Clone the repo
git clone --depth 1 https://github.com/TianGzlab/OmicsClaw

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for genomics-sv-detection

README.md
[![agentmods](https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-sv-detection/github.svg)](https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-sv-detection)
Your own site
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-sv-detection"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-sv-detection/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for genomics-sv-detection

Your own site · 80×15
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-sv-detection"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-sv-detection.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 78 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,155 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 1 finding, up to high

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • high Rogue Agent · line 3
    Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.
    Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00078 $0.01155
Opus 5 $0.00039 $0.00577
Sonnet 5 $0.00016 $0.00231
Haiku 4.5 $0.00008 $0.00115

Measured 9d ago against content hash 0f1df8c5d379, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

genomics-sv-detection scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (sv_detection.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/genomics/genomics-sv-detection/SKILL.md · 88 lines

How it starts

The opening of the file, as written. The whole thing — 88 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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

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.

Read the full file on GitHub · 88 lines

Files

What ships with it

5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 88 lines · 78 tokens per session scan A 0f1df8c5d379

Subscribe to this mod's changes

genomics-sv-detection is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 78 tokens to every session and 1,155 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientificbioinformaticsbnddellygenomicsknowledge-graphllm-agentmantamulti-agentsmulti-omicssnifflesstructural-variantssv
Related

Other skills, from other repositories

biomcp

Search and retrieve biomedical data - genes, variants, clinical trials, diagnostic tests, articles, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, and phenotype-disease matching. Use for gene function, variant pathogenicity, trials, diagnostics, drug safety, pathway context, disease workups…

genomoncology/biomcp · 70 tokens

biomcp-research

Do biomedical literature and variant research with the BioMCP CLI, and file what you learn about the tool itself as issues in the biomcp repo.

genomoncology/biomcp · 36 tokens

cellxgene-census-query

Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, and integrate with scanpy/PyTorch for population-scale single-cell analysis. Use this skill when: (1) Querying single-cell expression data by cell type, tissue, or disease, (2) Exploring available single-cell datasets…

PharMolix/OpenBioMed · 105 tokens

biological-expert

Expert-level biology, biotechnology, genetics, bioinformatics, and computational biology. Use when the user mentions biology, biotechnology, genetics, bioinformatics, or genomics, or when the task involves Molecular Biology, Genomics & Bioinformatics, Systems Biology, or Data Analysis.

personamanagmentlayer/pcl · 59 tokens

biotech-expert

Expert in biotechnology systems, genomics, LIMS, bioinformatics pipelines, lab automation, and bioprocess management. Use when the user mentions genomics, bioinformatics, LIMS, lab automation, bioprocessing, or gene sequencing, or when the task involves Genomics and Sequencing Technologies, Laboratory Information…

personamanagmentlayer/pcl · 83 tokens

nfcore-scrnaseq-wrapper

Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.

ClawBio/ClawBio · 55 tokens