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personal-genomics-analysis

Convert raw 23andMe genotype data into annotated genomic findings with SQLite databases.

Updated Mar 8, 2026
Search Tags:#sqlite#genomics#pharmacogenomics#personalized report#clinvar#23andme#ancestry analysis
One-click install
npx skills add https://github.com/ankitjh4/skill-builder --skill personal-genomics-analysis-ankitjh4
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: personal-genomics-analysis
Source: https://github.com/ankitjh4/skill-builder/tree/main/personal-genomics-analysis
Command: npx skills add https://github.com/ankitjh4/skill-builder --skill personal-genomics-analysis-ankitjh4

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

It solves the problem of turning raw 23andMe genotype files into an organized, queryable genomics dataset with annotated health risk, trait, ancestry, and drug-sensitivity insights.

Core Features & Use Cases

  • Personal genome database creation: Imports tab-delimited 23andMe SNP data into a local SQLite database for fast SNP queries and downstream analyses.
  • Clinical variant annotation: Downloads and indexes ClinVar data and cross-references SNPs to highlight pathogenic or likely pathogenic variants and associated diseases.
  • Pharmacogenomics interpretation: Uses PharmGKB-style drug-gene interaction mappings to surface drug sensitivities and evidence levels for common medications.
  • Trait, ancestry, and reporting outputs: Computes selected trait and ancestry markers and generates a personalized Markdown report with a summarized narrative plus supporting data structures.

Quick Start

Provide your 23andMe raw genotype file and run the pipeline to produce your local genome.db, ClinVar/PharmGKB lookups, and a personalized_genomics_report.md.

Frequently Asked Questions about personal-genomics-analysis

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

FAQPage Schema
How do I analyze my 23andMe raw genotype data for health risks and drug sensitivities?▼

To analyze 23andMe raw genotype data, you import the tab-delimited SNP file into a local SQLite database, cross-reference it with ClinVar and PharmGKB datasets, and generate a Markdown report highlighting pathogenic variants and drug sensitivities.

What is pharmacogenomics analysis and how does it apply to personalized genetic reports?▼

Pharmacogenomics analysis maps drug-gene interactions using PharmGKB-style data to surface medication sensitivities and evidence levels. Applied to personalized genetic reports, it summarizes actionable drug response insights based on your specific genotype markers.

Can I use my AncestryDNA file with this genomics analysis pipeline?▼

The pipeline requires tab-delimited input containing rsid, chromosome, position, and genotype fields. If your AncestryDNA file matches this formatting, it can be used to build the local genome database and run the ancestry composition estimation.

How do I find pathogenic variants in my raw DNA data using ClinVar?▼

Finding pathogenic variants requires downloading and indexing ClinVar data, then cross-referencing your SNP database against it to screen for pathogenic or likely pathogenic entries and their associated diseases.

What format does my genotype data need to be in for SNP database creation?▼

Genotype data must be a tab-delimited file containing rsid, chromosome, position, and genotype fields. This format is standard for 23andMe raw exports and is required to build the local SQLite genome database.

Does this genomics pipeline store my DNA data in the cloud?▼

No, the pipeline builds local SQLite databases including genome.db and indexed ClinVar/pharmgkb datasets on your machine. Your raw genotype data is processed and stored locally to generate the comprehensive Markdown report.

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