Detect Neanderthal and Denisovan introgression segments from modern human genomes
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Fire when:
Do NOT fire when:
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.
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).
# 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
Runs on bundled examples/demo_modern.vcf (3 samples, 10 SNPs on chr22) and
examples/demo_archaic.vcf (1 Neanderthal sample, same positions).
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 is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.
The agent dispatches queries and explains results. The skill executes the computational pipeline. The agent should not attempt to reimplement IBDmix LOD scoring outside this module.
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