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Genomics

Classify genomic variants from VCF files using ACMG/AMP guidelines.

Updated Apr 9, 2026
Search Tags:#genomics#pharmacogenomics#variant-interpretation#clinvar#acmg#gnomad#germline-somatic
One-click install
npx skills add https://github.com/jakechen1/echo-research-framework --skill genomics-jakechen1
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: Genomics
Source: https://github.com/jakechen1/echo-research-framework/tree/main/skills-available/genomics
Command: npx skills add https://github.com/jakechen1/echo-research-framework --skill genomics-jakechen1

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Interprets genomic variants by applying ACMG/AMP guidelines, pharmacogenomics insights, and assembling ClinVar/gnomAD annotations to support clinical decision-making from processed data.

Core Features & Use Cases

  • Variant classification using ACMG/AMP guidelines with triangulated evidence from ClinVar, gnomAD, and OMIM.
  • Pharmacogenomics interpretation including diplotype, predicted phenotype, affected drugs, and dosing considerations.
  • Annotates variants with clinically relevant information and clearly labels context (germline vs somatic) for reporting.
  • Local, privacy-preserving workflow with no automatic external API calls; enables manual lookup of external resources.
  • Use Case: A clinician reviews a VCF containing a BRCA1 variant to classify, annotate, and assess pharmacogenomic relevance where applicable.

Quick Start

Provide a VCF file and specify the interpretation context (germline or somatic) to begin a variant interpretation session.

Frequently Asked Questions about Genomics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I classify genomic variants from a VCF file using ACMG guidelines?▼

To classify genomic variants from a VCF, apply the ACMG/AMP guidelines while triangulating evidence from ClinVar, gnomAD, and OMIM to categorize findings and support clinical decision-making.

Can I analyze pharmacogenomics data and predict drug phenotypes from genomic variants?▼

Yes, pharmacogenomics analysis predicts phenotypes from diplotypes and identifies affected drugs alongside dosing considerations to guide clinical pharmacology decisions.

Does this variant interpretation workflow differentiate between germline and somatic contexts?▼

The workflow explicitly differentiates germline and somatic contexts, annotating findings with clinically relevant information and clear labels to ensure accurate clinical reporting.

What is the best way to annotate genomic variants without external API calls?▼

A local, privacy-preserving workflow annotates genomic variants without automatic external API calls, enabling manual lookup of external database resources like ClinVar and gnomAD.

Do I need a processed VCF to start clinical variant interpretation?▼

Yes, a processed VCF file is required to start clinical variant interpretation, alongside specifying the interpretation context as either germline or somatic.

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