# ClinPred missense pathogenicity scores, hg38, RM #37510

cd /hive/data/genomes/hg38/bed/clinPred

# Downloaded from https://sites.google.com/site/clinpred/ on May 5, 2026.
# The ClinPred site links to a Google Drive file; bypass the virus-scan
# interstitial with confirm=t to fetch directly:
curl -L -o ClinPred.txt \
    "https://drive.usercontent.google.com/download?id=1e0kd9hO1uCEuGzAhwEmLCNluqDFJE28y&export=download&confirm=t"

# Input is tab-separated: Chr Start Ref Alt ClinPred_Score (1-based positions,
# no chr prefix, three rows per scored exome position).
time python3 ~/kent/src/hg/makeDb/clinPred/clinPredToWig.py \
    /hive/data/genomes/hg38/chrom.sizes ClinPred.txt

wigToBigWig a.wig /hive/data/genomes/hg38/chrom.sizes a.bw &
wigToBigWig c.wig /hive/data/genomes/hg38/chrom.sizes c.bw &
wigToBigWig g.wig /hive/data/genomes/hg38/chrom.sizes g.bw &
wigToBigWig t.wig /hive/data/genomes/hg38/chrom.sizes t.bw &
wait
rm -f *.wig

# Color overlays generated with:
~/kent/src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py

# Install to /gbdb:
mkdir -p /gbdb/hg38/clinPred
ln -s /hive/data/genomes/hg38/bed/clinPred/{a,c,g,t}.bw /gbdb/hg38/clinPred/
ln -s /hive/data/genomes/hg38/bed/clinPred/{a,c,g,t}.color.bb /gbdb/hg38/clinPred/
