ensembl-vep-variant-annotator

Agent Skill: Clinical VCF Variant Prioritization & VEP Skill

📌 Description

Parses multi-sample VCF files, queries Ensembl VEP REST API, filters ClinVar pathogenicity ratings, and maps driver mutations to FDA targeted drugs.

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🤖 Agent Execution Protocol

When an AI Agent is tasked with ensembl-vep-variant-annotator:

1. Input Validation: Verify that the required input files or coordinates are supplied.
2. Environment Check: Ensure dependencies (PyVCF, Ensembl VEP API, ClinVar, Open Targets) are installed.
3. Execution: Run the protocol pipeline snippet below.
4. Output Generation: Produce actionable Markdown/JSON summaries with publication figures.

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💻 Protocol Code Snippet

import requests

def query_vep_variant(chrom, pos, ref, alt):
    url = f"https://rest.ensembl.org/vep/human/region/{chrom}:{pos}-{pos}:1/{alt}?content-type=application/json"
    r = requests.get(url)
    return r.json() if r.status_code == 200 else {}

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📥 Input & Output Specifications

Input Contract

• Target Files: Valid input data matching domain formats.
• Parameters: Quality thresholds and cutoffs.

Output Contract

• Results Table: Structured summary dataframe or matrix.
• Visualization: Rendered SVG/PNG figures.

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📄 License

Distributed under the MIT License. See LICENSE for details.