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genomics-variant-calling

genomics-variant-calling is a skill for Claude Code, Codex from TianGzlab/OmicsClaw. It costs 89 tokens per session (1,094 once invoked), scanned A, original, Apache-2.0.

A tool for summarising small DNA variants, such as single-letter changes and short insertions or deletions, from a VCF file. A VCF is a standard file that lists genetic variants found in sequencing data.

In plain words
What is it for?
Use it to count variants, split SNPs from indels, calculate the Ti/Tv ratio, and group variants by chromosome.
Why use it?
It provides common variant counts and distributions without running a separate variant-calling program.

Skill for Claude CodeCodex

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

not rated 160repo +1 1mo ago A scan 89 tokens original Apache-2.0

Good fit Use it to count variants, split SNPs from indels, calculate the Ti/Tv ratio, and group variants by chromosome.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/tiangzlab/omicsclaw/genomics-variant-calling
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-variant-calling
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-variant-calling

README.md
[![agentmods](https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-variant-calling.svg)](https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-variant-calling)
Your own site
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-variant-calling"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-variant-calling.svg" alt="Measured on agentmods" height="20"></a>
Per session 89 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,094 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.
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 $0.00089 $0.01094
Opus 5 $0.00044 $0.00547
Sonnet 5 $0.00018 $0.00219
Haiku 4.5 $0.00009 $0.00109

Measured 7d ago against content hash 2fcf4a67773c, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

genomics-variant-calling 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 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (genomics_variant_calling.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-variant-calling/SKILL.md · 92 lines

How it starts

The opening of the file, as written. The whole thing — 92 lines — stays where its author put it; the contents beside it link to each section on GitHub.

genomics-variant-calling

When to use

The user has a VCF (or a BAM intended for calling) and wants small-variant summary statistics: total variant count, SNP / indel split, Ti/Tv ratio, per-chromosome distribution. The script does not invoke an external caller (GATK HaplotypeCaller, Mutect2, DeepVariant, FreeBayes, etc.) — it summarises an existing VCF or generates a demo VCF for downstream-skill smoke tests.

For variant filtering / normalisation use genomics-vcf-operations; for SVs use genomics-sv-detection; for functional annotation use genomics-variant-annotation.

Inputs & Outputs

Inputs

  • File types: .vcf, .bam

Outputs

  • tables/variants.csv
  • tables/variants_per_chrom.csv
  • report.md
  • result.json
  • Produces artifact genomics.variant_table as tables/variants.csv (csv)

Flow

  1. Load VCF (--input <file.vcf>) or generate a demo VCF at output_dir/demo_variants.vcf with --n-variants records (genomics_variant_calling.py:94).
  2. Parse records; classify SNP vs indel; compute Ti/Tv on biallelic SNPs.
  3. Aggregate per-chromosome counts.
  4. Write tables/variants.csv (genomics_variant_calling.py:300) + tables/variants_per_chrom.csv (:308) + report.md + result.json envelope (:314).

Gotchas

  • No external caller is invoked. This skill does NOT run GATK / Mutect2 / DeepVariant / FreeBayes — it ingests a VCF and summarises it. To actually CALL variants, run an external pipeline first; this skill consumes the resulting VCF.
  • --input REQUIRED unless --demo. genomics_variant_calling.py:289 raises ValueError("--input required when not using --demo"); non-existent paths raise FileNotFoundError at :292.
  • --n-variants only affects --demo (genomics_variant_calling.py:278, default 500). It is silently ignored when --input is set.
  • Multi-allelic VCF rows ARE split per-ALT. genomics_variant_calling.py:181-182 iterates for a in alt.split(","): and emits one CSV row per ALT allele. Output row counts therefore exceed input VCF line counts on multi-allelic data — no need to pre-normalise unless your downstream consumer requires one row per VCF line.
  • Demo VCF is a minimal SNV set (no indels, no structural variants, no genotype fields). Useful for orchestrator smoke tests; do NOT use for biological inference.

Read the full file on GitHub · 92 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. 7d ago First seen · 92 lines · 89 tokens per session scan A 2fcf4a67773c

Subscribe to this mod's changes

genomics-variant-calling is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 89 tokens to every session and 1,094 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.

ScientificSingle-Cellbioinformaticsgenomicsindelknowledge-graphllm-agentmulti-agentsmulti-omicssnvti-tvvariant-callingvcf
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