Archaic Introgression Detector

Trigger

Fire when:

• User asks about Neanderthal or Denisovan DNA in modern humans
• User wants to detect archaic introgression segments
• User mentions IBDmix, Sprime, or hmmix methods
• User has modern + archaic VCF files and wants to compare them

Do NOT fire when:

• User asks about general ancestry or population structure (use claw-ancestry-pca)
• User asks about pharmacogenomics or clinical variants
• User wants admixture proportions without segment-level detail

Why This Exists

Between 1-4% of non-African modern human genomes derive from archaic hominins (Neanderthals, Denisovans). Identifying these segments matters for understanding human evolution, disease susceptibility, and immune adaptation. Three complementary methods exist (IBDmix, Sprime, hmmix), each with different strengths. This skill wraps all three behind a unified interface with a pure-Python fallback when external binaries are unavailable.

Core Capabilities

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

Scope

One skill, one task: detect and report archaic introgression segments. Does not perform downstream functional annotation of introgressed variants (chain with vcf-annotator for that).

Input Formats

• Modern genotypes: VCF (uncompressed or .vcf.gz with .tbi index)
• Archaic genotypes: VCF (Neanderthal/Denisovan reference panel)
• EIGENSTRAT: .ind + .snp + .geno files (text or binary packed format)

Workflow