ce180274fa3ba3db5c10ecbd9ae2479d4816e972
max
  Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies

Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/hg38/mpravardb.txt src/hg/makeDb/doc/hg38/mpravardb.txt
new file mode 100644
index 00000000000..f3305f0414b
--- /dev/null
+++ src/hg/makeDb/doc/hg38/mpravardb.txt
@@ -0,0 +1,22 @@
+# MPRAVarDB track
+# Mon Mar 10 2026 (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
+
+# The file mpravardb.csv was downloaded from the MPRAVarDB website.
+# 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)
+
+# Create gbdb symlink
+mkdir -p /gbdb/hg38/mpra
+ln -sf /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb /gbdb/hg38/mpra/mpravardb.bb
+
+# Rebuild trackDb
+cd ~/kent/src/hg/makeDb/trackDb
+make DBS=hg38