Archaic Introgression

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/archaic-introgression”

Requirements

• Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1IBDmix: Detect segments shared IBD between modern and archaic genomes using LOD score thresholds
2. 2Sprime: Identify introgressed haplotypes without requiring an archaic reference panel
3. 3hmmix: HMM-based detection of archaic ancestry tracts
4. 4Pure-Python fallback: LOD-score-based segment calling when IBDmix binary is not installed
5. 5EIGENSTRAT support: Read .ind/.snp/.geno files (text and binary packed formats)
6. 6Summary statistics: Per-individual introgression burden, segment count, mean length

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Archaic Introgression loads about 1.9k tokens when it runs. Until then it costs about 26 tokens; SKILL.md has 710 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~26

When it runs · the whole SKILL.md, loaded when a task matches

~1.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 710 words, ~1,894 tokens.

name

archaic-introgression

description

Detect Neanderthal and Denisovan introgression segments from modern human genomes

license

MIT

metadata.version

0.1.0

metadata.author

Manuel Corpas

metadata.domain

genomics

# Run with IBDmix on VCF inputs
python archaic_introgression.py \
  --input modern.vcf --archaic archaic.vcf \
  --method ibdmix --output /tmp/introgression

# Run demo with synthetic data
python archaic_introgression.py --demo --output /tmp/introgression_demo

# Filter to specific samples
python archaic_introgression.py \
  --input modern.vcf --archaic archaic.vcf \
  --samples SAMPLE01,SAMPLE02 --output /tmp/introgression

# Adjust LOD threshold
python archaic_introgression.py \
  --input modern.vcf --archaic archaic.vcf \
  --lod 5.0 --output /tmp/introgression

python archaic_introgression.py --demo --output /tmp/introgression_demo

output_dir/
  introgression_results.json   # Full results with segments and summary
  segments.bed                 # BED file of introgressed regions

{
  "method": "ibdmix",
  "lod_threshold": 3.0,
  "num_samples": 3,
  "segments": [
    {
      "sample": "SAMPLE01",
      "chrom": "chr22",
      "start": 16050075,
      "end": 16051249,
      "archaic_source": "Neanderthal",
      "method": "ibdmix",
      "score": 4.2,
      "num_variants": 6,
      "length": 1174
    }
  ],
  "summary": {
    "SAMPLE01": {
      "total_segments": 1,
      "total_length_bp": 1174,
      "mean_segment_length": 1174.0,
      "mean_score": 4.2
    }
  }
}

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 7 other files in skills/archaic-introgression of ClawBio/ClawBio.

• SKILL.md
• archaic_introgression.py
• examples/demo_archaic.vcf
• examples/demo_modern.vcf
• pipeline.py
• tests/__init__.py
• tests/test_archaic_introgression.py
• tests/test_pipeline.py

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

• BioTender-max/awesome-bio-agent-skillsskills/clawbio/archaic-introgression