2a58182f173ac7c5b7f28e39835ae79e4fe78466
max
  Mon Feb 23 04:12:52 2026 -0800
making gnomad coverage on hg38 always start at 0, feedback from Alistair Pagnamenta, refs #37041

diff --git src/hg/makeDb/doc/hg38/gnomad.txt src/hg/makeDb/doc/hg38/gnomad.txt
index 4a46431a568..f5c7829c9d4 100644
--- src/hg/makeDb/doc/hg38/gnomad.txt
+++ src/hg/makeDb/doc/hg38/gnomad.txt
@@ -705,33 +705,47 @@
 # gnomAD Coverage v3.0.1 - Jan 28, 2026 - max
 ##############################################################################
 # Coverage data from gnomAD genomes v3.0.1
 # Source: https://gnomad.broadinstitute.org/downloads#v3-coverage
 
 cd /hive/data/genomes/hg38/bed/gnomad/coverage/v3-genome
 
 # Download coverage summary file
 wget https://storage.googleapis.com/gcp-public-data--gnomad/release/3.0.1/coverage/genomes/gnomad.genomes.r3.0.1.coverage.summary.tsv.bgz
 
 # Convert TSV to bigWig files using Python script
 python3 ~/kent/src/hg/makeDb/scripts/gnomadCovToBw.py gnomad.genomes.r3.0.1.coverage.summary.tsv.bgz
 # Creates 11 bigWig files
 
 # Create symlinks in /gbdb
-mkdir -p /gbdb/hg38/gnomAD/coverage/v3-genome/
-cd /gbdb/hg38/gnomAD/coverage
-for f in /hive/data/genomes/hg38/bed/gnomad/coverage/*.bw; do ln -sf "$f" .; done
+mkdir -p /gbdb/hg38/gnomAD/coverage/v3-genome
+cd /gbdb/hg38/gnomAD/coverage/v3-genome
+for f in /hive/data/genomes/hg38/bed/gnomad/coverage/v3-genome/gnomad.coverage.*.bw; do ln -sf "$f" .; done
 
 ##############################################################################
 # gnomAD Exome Coverage v4 - Jan 29, 2026 - max
 ##############################################################################
 # Coverage data from gnomAD exomes v4
 # Source: https://gnomad.broadinstitute.org/downloads#v4-coverage
 
 cd /hive/data/genomes/hg38/bed/gnomad/coverage/v4-exome/
 
 # Download coverage summary file
 aria2c -x10 https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/coverage/exomes/gnomad.exomes.v4.0.coverage.summary.tsv.bgz
 
 # Convert TSV to bigWig files using Python script
 python3 ~/kent/src/hg/makeDb/scripts/gnomadCovToBw.py gnomad.exomes.v4.0.coverage.summary.tsv.bgz
-# Creates 11 bigWig files
+# Creates 11 bigWig files:
+#   gnomad.coverage.mean.bw, gnomad.coverage.median.bw,
+#   gnomad.coverage.over_{1,5,10,15,20,25,30,50,100}.bw
+# Note: The script handles chromosome ordering (gnomAD uses chr1-22,X,Y,M order,
+# not the chrom.sizes order) and skips duplicate positions in the input data.
+# Processed 170,202,927 lines, skipped 2 duplicate positions.
+
+# Create symlinks in /gbdb
+mkdir -p /gbdb/hg38/gnomAD/coverage/v4-exome
+cd /gbdb/hg38/gnomAD/coverage/v4-exome
+for f in /hive/data/genomes/hg38/bed/gnomad/coverage/v4-exome/gnomad.coverage.*.bw; do ln -sf "$f" .; done
+
+# Add track to trackDb (gnomadCoverage.ra) and rebuild
+cd ~/kent/src/hg/makeDb/trackDb
+make DBS=hg38