genome-analizer_skill

Overview

This skill analyzes a user's genetic data from a VCF file to provide clear, practical interpretations about inherited traits, disease risks, metabolism, and personalized recommendations. It finds relevant SNPs for a user question, extracts genotypes from the VCF, and maps them to known allele effects. The output is a structured, user-friendly report focused on actionable insights rather than raw data.

How this skill works

First, the skill searches the current directory for VCF files and asks which file to use if several are found. It then runs a focused search for SNPs (rsIDs) and gene associations relevant to the user's topic using curated sources like GWAS Catalog and SNPedia. Next it locates those rsIDs in the selected VCF, decodes genotypes (0/0, 0/1, 1/1) and interprets each in light of the allele effect evidence. Finally, it generates a concise, practitioner-style report with practical recommendations.

When to use it

• You have a VCF file and want an understandable summary of relevant genetic variants
• You ask about genetic predisposition to a disease, metabolism, or traits
• You want genotype-based nutrition, drug, or lifestyle recommendations
• You need a clear mapping from rsIDs to your VCF genotypes
• You want a short, actionable report rather than raw variant lists

Best practices

• Provide a clear question or topic (e.g., caffeine metabolism, heart disease risk)
• Supply the VCF in the current working directory before starting
• Be aware the tool reports probabilities and associations, not diagnoses
• Request follow-up on any variant you find unclear or clinically relevant
• Use the results to guide discussions with a qualified clinician for medical decisions

Example use cases

• Assess caffeine sensitivity by searching for CYP1A2 and related SNPs
• Check pharmacogenetic markers for common drug responses
• Review genetic risk factors for cardiovascular disease and practical lifestyle steps
• Explore genetic contributors to athletic performance or recovery
• Identify potential lactose or other food intolerance markers for diet planning