What is bio-clinical-databases-dbsnp-queries?

A workflow for looking up genetic variant identifiers and converting between formats such as rsIDs, HGVS, SPDI, and VCF. dbSNP is a public database of small genetic differences, and rsIDs are its reference labels.

Use it to normalise variant lists, follow rsID merge histories, and convert variant representations for database matching.

It resolves outdated or merged identifiers and makes variant records from different tools easier to join reliably.

bio-clinical-databases-dbsnp-queries — Skill for Claude Code and Codex

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 GPTomics/bioSkills --skill dbsnp-queries

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/dbsnp-queries/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/dbsnp-queries)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/dbsnp-queries"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/dbsnp-queries/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/dbsnp-queries"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/dbsnp-queries.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 79 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 5,391 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. 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.

Model	Per session	Once invoked
Fable 5.1	$0.00079	$0.05391
Opus 5	$0.00039	$0.02695
Sonnet 5	$0.00016	$0.01078
Haiku 4.5	$0.00008	$0.00539

Measured 7d ago against content hash a7e4727f9aa8, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

bio-clinical-databases-dbsnp-queries scanned grade A with 1 finding 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 (examples/dbsnp_lookup.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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- Python (direct): `requests.get(f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_int}')`

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-clinical-databases-dbsnp-queries — 95% identical, 12 lines differ

clinical-databases/dbsnp-queries/SKILL.md · 337 lines

How it starts

The opening of the file, as written. The whole thing — 337 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: myvariant 1.0+, requests 2.31+, biopython 1.83+, Entrez Direct 21.0+. dbSNP Build 156 (September 2022) is the current schema; Build 151 (2017) was the last with relational SQL dumps. Builds 152-155 dual-released JSON+SQL; 156+ is JSON-only.

Before using code patterns, verify installed versions match. If versions differ:

Python: pip show <package> then help(module.function) to check signatures
CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. The Variation Services REST API uses path-based versioning (/variation/v0/); E-utilities db=snp returns thin legacy summaries missing build-156 schema fields.

dbSNP Queries and rsID Normalization

'Look up this rsID / normalize variant representations' -> Resolve rsIDs through merge chains, compute canonical SPDI, and convert between rsID, HGVS-g, HGVS-c, and VCF allele representations.

Python (aggregator): myvariant.MyVariantInfo().getvariant(rsid, fields=['dbsnp', 'clinvar', 'gnomad_exome'])
Python (direct): requests.get(f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_int}')
Python (E-utilities, legacy): Bio.Entrez.esearch(db='snp', term=rsid); returns thin summary
Bulk: ftp.ncbi.nlm.nih.gov/snp/latest_release/JSON/refsnp-chr{N}.json.bz2

rsID Is a Cluster Identifier, Not a Variant Identifier

This is the load-bearing concept. dbSNP cluster definition: ss records (submitted SNPs) are mapped to the genome and clustered into RefSNPs by position + variant type, not by allele. A single rsID can point to a locus with multiple alleles:

rs12345 may resolve to {A>G, A>T, A>C} at one position; the RefSNP JSON primary_snapshot_data.placements_with_allele[*].alleles enumerates them.
~6-8% of dbSNP rsIDs are multi-allelic.
PLINK and many older tools historically misuse rsIDs as if they were variant identifiers, which fails for multi-allelic sites and yields wrong genotype assignments.

Read the full file on GitHub · 337 lines

Files

What ships with it

2 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.

7d ago First seen · 337 lines · 79 tokens per session scan A a7e4727f9aa8

Subscribe to this mod's changes

bio-clinical-databases-dbsnp-queries is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 79 tokens to every session and 5,391 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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