684ad73a17eebb717fba52f0aa25f3d9d7adb2de
max
  Thu Sep 3 12:03:37 2026 -0700
New Imprinting track collection on hg38, first subtrack is MethBase2 ASM

Adds the "Imprinting" superTrack to the Regulation group and its first
subtrack, the allele-specific methylation summary from the MethBase2 hub
(http://smithlab.usc.edu/trackdata/methylation/hub.txt). The bigWig gives,
for each of 29,401,795 CpG sites, the fraction of MethBase2 human methylomes
in which the site fell inside an allelically methylated region called by
dnmtools amrfinder. Taken from upstream unchanged.

Alpha only for now, refs #37599

diff --git src/hg/makeDb/doc/hg38/imprinting.txt src/hg/makeDb/doc/hg38/imprinting.txt
new file mode 100644
index 00000000000..96b313896ea
--- /dev/null
+++ src/hg/makeDb/doc/hg38/imprinting.txt
@@ -0,0 +1,53 @@
+# Imprinting track collection on hg38, refs #37599
+# 2026-09-03 Claude-max
+
+# The "Imprinting" superTrack collects annotations of imprinted loci and of the
+# allele-specific methylation that marks them.
+
+##############################################################################
+# MethBase2 ASM - allele-specific methylation fraction across methylomes
+# (refs #37599, data source is the MethBase2 hub, refs #36320)
+##############################################################################
+
+# The MethBase2 track hub (Andrew D. Smith, USC) publishes an assembly-wide
+# summary bigWig under its "common" section. For each CpG site it holds the
+# fraction of MethBase2 hg38 methylomes in which that site fell inside an
+# allelically methylated region called by "dnmtools amrfinder".
+#
+#   hub:  http://smithlab.usc.edu/trackdata/methylation/hub.txt
+#   file: http://smithlab.usc.edu/methbase/data/common/hg38/hg38.asm.bw
+#
+# We take the file as-is. No conversion, filtering or recalculation is done.
+
+mkdir -p /hive/data/genomes/hg38/bed/imprinting/methBaseAsm
+cd /hive/data/genomes/hg38/bed/imprinting/methBaseAsm
+curl -sS -O http://smithlab.usc.edu/methbase/data/common/hg38/hg38.asm.bw
+
+# The upstream file was last modified 2025-07-14 and is 163,160,098 bytes.
+# Sanity checks: hg38 chrom names and sizes, value range, coverage.
+
+bigWigInfo hg38.asm.bw
+# chromCount: 25
+# basesCovered: 29,401,795
+# mean: 0.000728
+# min: 0.000000
+# max: 0.862512
+# std: 0.009708
+
+# 25 chroms = chr1-chr22, chrX, chrY, chrM, all with hg38 sizes. All values are
+# fractions in [0,1]. basesCovered equals the number of annotated CpG positions,
+# each a single-base interval. Nothing is outside a chrom boundary, nothing was
+# skipped.
+
+# Spot check three loci: the H19/IGF2 imprinting control region, the
+# SNRPN/PWS-AS region, and a non-imprinted control region on chr20.
+
+for r in "chr11 1990000 2010000" "chr15 24954000 25200000" "chr20 57414000 57430000"; do
+    set -- $r
+    echo "== $1:$2-$3"
+    bigWigToBedGraph -chrom=$1 -start=$2 -end=$3 hg38.asm.bw stdout \
+        | sort -k4,4gr | head -3
+done
+# chr11:1,999,937  0.4886   <- H19 ICR, as expected
+# chr15:24,955,342 0.5362   <- SNRPN/MAGEL2 region, as expected
+# chr20:57,428,788 0.0006   <- control, essentially zero