9e4b6bdfe320b9def27f549f4928392e2b4d0937
max
  Mon Apr 13 08:35:23 2026 -0700
Add BCGSC Human BAC Re-Array (32k set) track on hg38, refs #35059

New subtrack under cloneEndSuper showing the curated 32k BAC clone tiling
path provided by BACPAC Genomics (CHORI). Data is the pre-lifted hg38
custom track from bacpacresources.org, converted to bigBed5.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/hg38/bacRearray32k.txt src/hg/makeDb/doc/hg38/bacRearray32k.txt
new file mode 100644
index 00000000000..493a3ab4301
--- /dev/null
+++ src/hg/makeDb/doc/hg38/bacRearray32k.txt
@@ -0,0 +1,20 @@
+# BCGSC Human BAC Re-Array "32k set" track, refs #35059 (Claude)
+Mon Apr 13 2026 (Claude, max)
+
+# Source: pre-lifted hg38 BED5 custom track provided by Pieter de Jong / BACPAC
+# Genomics at CHORI.  Clone placements were originally liftover'd from hg18 by
+# BACPAC.
+
+mkdir -p /hive/data/genomes/hg38/bed/bacRearray32k
+cd /hive/data/genomes/hg38/bed/bacRearray32k
+
+# Download the pre-lifted custom track file
+curl -s -o humanbacs.hg38.track \
+    https://bacpacresources.org/download/humanbacHg18To38/humanbacs.hg38.track
+
+# Strip the "browser" and "track" header lines, sort, convert to bigBed 5.
+grep -v '^browser\|^track' humanbacs.hg38.track \
+    | sort -k1,1 -k2,2n > bacRearray32k.sorted.bed
+
+bedToBigBed -type=bed5 bacRearray32k.sorted.bed \
+    /hive/data/genomes/hg38/chrom.sizes bacRearray32k.bb