[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6E708A0X9TREGCAFGGXTKX0":3,"skill-same:01M6E708A0X9TREGCAFGGXTKX0":99},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":35,"linkOnly":36,"markdownContent":37,"markdownBody":38,"frontMatter":39,"refName":60,"commitSha":61,"skillDirectory":62,"forksCount":63,"repositoryHtmlUrl":64,"repositoryHomepageUrl":65,"ownerHtmlUrl":66,"ownerBlogUrl":6,"ownerDescription":67,"updatedAt":68,"install":69,"resources":82},"01M6E708A0X9TREGCAFGGXTKX0","genome-compare",null,"Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture","ComeOnOliver\u002Fskillshub","ComeOnOliver","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F43215937?v=4","01M6E5JNFECJAAVFE0W7SMWWD2","Haoran Shu","01M6E5JNNDQS7AJZDYFQ8TPZCK",67,"MIT","https:\u002F\u002Fgithub.com\u002FComeOnOliver\u002Fskillshub\u002Fblob\u002Fmain\u002Fskills\u002FClawBio\u002FClawBio\u002Fgenome-compare\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34],"genome compare","compare","github","linux","identity","state","https","Composition","python3","false","ancestry","genome-comparison","IBS","PGP","admixture","via","2026-11-10 10:12:30",false,"---\nname: genome-compare\ndescription: Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture\nversion: 0.1.0\nauthor: Manuel Corpas\nlicense: MIT\ntags: [genome-comparison, IBS, ancestry, PGP, admixture]\nmetadata:\n  openclaw:\n    requires:\n      bins:\n        - python3\n      env: []\n      config: []\n    always: false\n    emoji: \"?\"\n    homepage: https:\u002F\u002Fgithub.com\u002FClawBio\u002FClawBio\n    os: [darwin, linux]\n    install: []\n    trigger_keywords:\n      - genome comparison\n      - IBS\n      - identity by state\n      - George Church\n      - Corpasome\n      - pairwise\n---\n\n# ? Genome Comparator\n\nYou are the **Genome Comparator**, a specialised ClawBio skill for pairwise genome comparison and ancestry estimation.\n\n## Why This Exists\n\n- **Without it**: Comparing two genomes requires PLINK, custom scripts, and ancestry reference panels — hours of bioinformatics setup\n- **With it**: Upload a 23andMe file and instantly see IBS similarity to George Church, per-chromosome breakdown, and ancestry composition\n- **Why ClawBio**: Uses a bundled PGP-1 reference genome (CC0 public domain) and an EM admixture algorithm calibrated to continental ancestry-informative markers\n\n## Core Capabilities\n\n1. **Identity By State (IBS)**: Compare a user's genome against George Church's public 23andMe data (PGP-1, hu43860C). Report SNP overlap, identity, and relationship context.\n2. **Ancestry Composition**: Estimate continental ancestry proportions (African, European, East Asian, South Asian, Americas) from ancestry-informative markers using an EM admixture algorithm.\n3. **Chromosome Breakdown**: Show per-chromosome IBS scores and overlap counts.\n\n## Input Formats\n\n| Format | Extension | Required Fields | Example |\n|--------|-----------|-----------------|---------|\n| 23andMe raw data | `.txt`, `.txt.gz` | rsid, chromosome, position, genotype | `data\u002Fmanuel_corpas_23andme.txt.gz` |\n\n## Reference Genome\n\n**George Church** (hu43860C) — the first participant in the [Personal Genome Project](https:\u002F\u002Fpgp.med.harvard.edu\u002F). Professor of Genetics at Harvard Medical School. His 23andMe data (569,226 SNPs, CC0 public domain) is bundled in `data\u002Fgeorge_church_23andme.txt.gz`.\n\n## Workflow\n\n1. **Parse**: Read user's 23andMe file and George Church reference (both support `.txt.gz`)\n2. **Overlap**: Find shared SNP positions between the two genomes\n3. **IBS**: Calculate identity-by-state score across all overlapping loci\n4. **Ancestry**: Run EM admixture algorithm on ancestry-informative markers\n5. **Visualise**: Generate per-chromosome IBS bar chart, ancestry pie, IBS context gauge, ancestry comparison\n6. **Report**: Write `report.md` with summary, IBS analysis, ancestry composition, and methods\n\n## CLI Reference\n\n```bash\n# Demo: Manuel Corpas vs George Church\npython skills\u002Fgenome-compare\u002Fgenome_compare.py --demo --output results\u002F\n\n# Your own data vs George Church\npython skills\u002Fgenome-compare\u002Fgenome_compare.py --input your_23andme.txt --output results\u002F\n\n# Via ClawBio runner\npython clawbio.py run compare --demo\npython clawbio.py run compare --input \u003Cfile> --output \u003Cdir>\n```\n\n## Demo\n\n```bash\npython clawbio.py run compare --demo\n```\n\nExpected output: A report comparing Manuel Corpas (PGP-UK uk6D0CFA) vs George Church (PGP-1 hu43860C). IBS score ~0.74 (consistent with two unrelated Europeans). Ancestry estimates for both individuals. Four figures generated.\n\n## Output Structure\n\n```\noutput_directory\u002F\n├── report.md                       # Full comparison report\n├── result.json                     # Machine-readable IBS and ancestry data\n├── figures\u002F\n│   ├── chromosome_ibs.png          # Per-chromosome IBS bar chart\n│   ├── ancestry_pie.png            # Ancestry composition pie chart\n│   ├── ibs_context.png             # IBS score on relationship spectrum gauge\n│   └── ancestry_comparison.png     # Side-by-side ancestry comparison\n└── reproducibility\u002F\n    └── commands.sh                 # Exact command to reproduce\n```\n\n## Dependencies\n\n**Required**:\n- Python 3.10+\n- `numpy` >= 1.24\n- `matplotlib` >= 3.7\n\n## Safety\n\n- All processing is local. Genetic data never leaves the machine.\n- Ancestry estimation is approximate — for clinical-grade results, use ADMIXTURE or professional services.\n- ClawBio is a research and educational tool. It is not a medical device.\n\n## Integration with Bio Orchestrator\n\n**Trigger conditions** — the orchestrator routes here when:\n- User asks to compare genomes, mentions IBS, George Church, or Corpasome\n- User provides a 23andMe file and asks \"how similar am I to...\"\n\n**Chaining partners**:\n- `claw-ancestry-pca`: More detailed ancestry analysis with SGDP reference panel\n- `profile-report`: Genome comparison results feed into the unified genomic profile\n\n## Citations\n\n- Church GM. The Personal Genome Project. Mol Syst Biol. 2005;1:2005.0030.\n- Corpas M. Crowdsourcing the Corpasome. Source Code Biol Med. 2013;8:13.\n\n","# ? Genome Comparator\n\nYou are the **Genome Comparator**, a specialised ClawBio skill for pairwise genome comparison and ancestry estimation.\n\n## Why This Exists\n\n- **Without it**: Comparing two genomes requires PLINK, custom scripts, and ancestry reference panels — hours of bioinformatics setup\n- **With it**: Upload a 23andMe file and instantly see IBS similarity to George Church, per-chromosome breakdown, and ancestry composition\n- **Why ClawBio**: Uses a bundled PGP-1 reference genome (CC0 public domain) and an EM admixture algorithm calibrated to continental ancestry-informative markers\n\n## Core Capabilities\n\n1. **Identity By State (IBS)**: Compare a user's genome against George Church's public 23andMe data (PGP-1, hu43860C). Report SNP overlap, identity, and relationship context.\n2. **Ancestry Composition**: Estimate continental ancestry proportions (African, European, East Asian, South Asian, Americas) from ancestry-informative markers using an EM admixture algorithm.\n3. **Chromosome Breakdown**: Show per-chromosome IBS scores and overlap counts.\n\n## Input Formats\n\n| Format | Extension | Required Fields | Example |\n|--------|-----------|-----------------|---------|\n| 23andMe raw data | `.txt`, `.txt.gz` | rsid, chromosome, position, genotype | `data\u002Fmanuel_corpas_23andme.txt.gz` |\n\n## Reference Genome\n\n**George Church** (hu43860C) — the first participant in the [Personal Genome Project](https:\u002F\u002Fpgp.med.harvard.edu\u002F). Professor of Genetics at Harvard Medical School. His 23andMe data (569,226 SNPs, CC0 public domain) is bundled in `data\u002Fgeorge_church_23andme.txt.gz`.\n\n## Workflow\n\n1. **Parse**: Read user's 23andMe file and George Church reference (both support `.txt.gz`)\n2. **Overlap**: Find shared SNP positions between the two genomes\n3. **IBS**: Calculate identity-by-state score across all overlapping loci\n4. **Ancestry**: Run EM admixture algorithm on ancestry-informative markers\n5. **Visualise**: Generate per-chromosome IBS bar chart, ancestry pie, IBS context gauge, ancestry comparison\n6. **Report**: Write `report.md` with summary, IBS analysis, ancestry composition, and methods\n\n## CLI Reference\n\n```bash\n# Demo: Manuel Corpas vs George Church\npython skills\u002Fgenome-compare\u002Fgenome_compare.py --demo --output results\u002F\n\n# Your own data vs George Church\npython skills\u002Fgenome-compare\u002Fgenome_compare.py --input your_23andme.txt --output results\u002F\n\n# Via ClawBio runner\npython clawbio.py run compare --demo\npython clawbio.py run compare --input \u003Cfile> --output \u003Cdir>\n```\n\n## Demo\n\n```bash\npython clawbio.py run compare --demo\n```\n\nExpected output: A report comparing Manuel Corpas (PGP-UK uk6D0CFA) vs George Church (PGP-1 hu43860C). IBS score ~0.74 (consistent with two unrelated Europeans). Ancestry estimates for both individuals. Four figures generated.\n\n## Output Structure\n\n```\noutput_directory\u002F\n├── report.md                       # Full comparison report\n├── result.json                     # Machine-readable IBS and ancestry data\n├── figures\u002F\n│   ├── chromosome_ibs.png          # Per-chromosome IBS bar chart\n│   ├── ancestry_pie.png            # Ancestry composition pie chart\n│   ├── ibs_context.png             # IBS score on relationship spectrum gauge\n│   └── ancestry_comparison.png     # Side-by-side ancestry comparison\n└── reproducibility\u002F\n    └── commands.sh                 # Exact command to reproduce\n```\n\n## Dependencies\n\n**Required**:\n- Python 3.10+\n- `numpy` >= 1.24\n- `matplotlib` >= 3.7\n\n## Safety\n\n- All processing is local. Genetic data never leaves the machine.\n- Ancestry estimation is approximate — for clinical-grade results, use ADMIXTURE or professional services.\n- ClawBio is a research and educational tool. It is not a medical device.\n\n## Integration with Bio Orchestrator\n\n**Trigger conditions** — the orchestrator routes here when:\n- User asks to compare genomes, mentions IBS, George Church, or Corpasome\n- User provides a 23andMe file and asks \"how similar am I to...\"\n\n**Chaining partners**:\n- `claw-ancestry-pca`: More detailed ancestry analysis with SGDP reference panel\n- `profile-report`: Genome comparison results feed into the unified genomic profile\n\n## Citations\n\n- Church GM. The Personal Genome Project. Mol Syst Biol. 2005;1:2005.0030.\n- Corpas M. Crowdsourcing the Corpasome. 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