# PrimateAI-3D, Claude max, Mar 19 2026

# Source: PrimateAI-3D.hg38.txt.gz from https://primateai3d.basespace.illumina.com/
# 70.7M missense variant pathogenicity predictions

cd /hive/data/genomes/hg38/bed/primateai
# download PrimateAI-3D.hg38.txt.gz from Illumina BaseSpace (requires registration)

# convert to BED (1-based input -> 0-based BED), colored by percentile (blue=benign, red=pathogenic)
python3 ~/kent/src/hg/makeDb/scripts/primateai/primateAiToBigBed.py
# 70,667,466 variants written

# sort and convert to bigBed
sort -k1,1 -k2,2n primateAi.bed > primateAi.sorted.bed
bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/primateai/primateAi.as -tab \
    primateAi.sorted.bed /hive/data/genomes/hg38/chrom.sizes primateAi.bb
rm primateAi.bed primateAi.sorted.bed
