# max Mar 30 2026
# There was nothing to do, Varda from the Ahituv Lab provided the bigBed file at
# https://genome.ucsc.edu/hubspace/72/Varda006/Varda_Final_Hub/final_authorPMID.mean_v2.bb
# and a hub at https://genome.ucsc.edu/hubspace/72/Varda006/Varda_Final_Hub/hub.txt

# MPRAVarDB track
# Mon Mar 10 2026 (claude/max)

# Download data from https://mpravardb.rc.ufl.edu/
mkdir -p /hive/data/genomes/hg38/bed/mpra/mpravardb
cd /hive/data/genomes/hg38/bed/mpra/mpravardb
wget 'https://mpravardb.rc.ufl.edu/session/27d7af46df917aed91f4cca7bee378a2/download/download_all?w=' -O mpravardb.csv

# 242,818 variants from 18 MPRA studies, with both hg19 and hg38 coordinates.
# 213,689 are hg19, 29,129 are hg38, 3,676 have no coordinates (NA).

# Convert to BED, liftOver hg19->hg38, merge, and create bigBed:
python3 ~/kent/src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
# Output: mpravardb.bb (239,028 variants after liftOver, 114 unmapped)
