f20626542200362afacab9387842e1f5bb50c87c
chmalee
  Fri Sep 25 12:43:42 2026 -0700
Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617

diff --git src/hg/makeDb/scripts/gnomadV4.1.1/loadGnomadV4.1.1ChromTables.sh src/hg/makeDb/scripts/gnomadV4.1.1/loadGnomadV4.1.1ChromTables.sh
new file mode 100755
index 00000000000..d157cf8c2f7
--- /dev/null
+++ src/hg/makeDb/scripts/gnomadV4.1.1/loadGnomadV4.1.1ChromTables.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+# loadGnomadV4.1.1ChromTables.sh -- build and hgLoadSqlTab the per-chrom
+# vcfTabix lookup tables (bbiChroms schema) for the gnomAD v4.1.1
+# exomes and genomes vcfTabix children. Idempotent: rerunning replaces
+# the table contents.
+#
+# Usage: loadGnomadV4.1.1ChromTables.sh [DB]
+#   DB defaults to hg38.
+#
+# Pre-req: /gbdb symlinks at /gbdb/hg38/gnomAD/v4.1.1/{exomes,genomes}/
+# already in place.
+
+set -euo pipefail
+
+DB="${1:-hg38}"
+SCHEMA=$HOME/kent/src/hg/lib/bbiChroms.sql
+WORKDIR=$(mktemp -d)
+trap 'rm -rf "$WORKDIR"' EXIT
+
+CHROMS="1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y"
+
+for ds in exomes genomes; do
+    table="gnomad${ds^}V4_1_1Vcf"       # gnomadExomesV4_1_1Vcf / gnomadGenomesV4_1_1Vcf
+    tsv="${WORKDIR}/${table}.txt"
+    : > "$tsv"
+    for chr in $CHROMS; do
+        printf '/gbdb/%s/gnomAD/v4.1.1/%s/gnomad.%s.v4.1.1.sites.chr%s.vcf.bgz\tchr%s\n' \
+            "$DB" "$ds" "$ds" "$chr" "$chr" >> "$tsv"
+    done
+    echo "Loading $table from $tsv ($(wc -l < "$tsv") rows)"
+    hgLoadSqlTab "$DB" "$table" "$SCHEMA" "$tsv"
+done
+
+echo "done"