f665d4cc3b02924a8507b2f910eaf85eab54d433
braney
  Sat Jul 18 14:12:24 2026 -0700
hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts

Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to
test left-shifting indel placement and to measure how the deletions correspond
to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded
left-normalizer, the aggregation and subsampling drivers, the stability and
cross-release carryover analyses, and the dbSNP rs cross-reference prototype.
See README.txt for the manifest; full results and cached data live in
/hive/data/genomes/hg38/bed/hprc2X.

refs #37891

diff --git src/hg/makeDb/scripts/hprc2X/hprc2XIndelsOne.sh src/hg/makeDb/scripts/hprc2X/hprc2XIndelsOne.sh
new file mode 100755
index 00000000000..0f9385219a0
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2X/hprc2XIndelsOne.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+# Regenerate the per-assembly indel intermediate for the hprc2X track set, this
+# time left-normalizing pure deletions against the hg38 target sequence
+# (chainInDel -t2bit).  Everything else the hprc2 build produced (chain/net,
+# bigChains, inversions, duplications) is reused unchanged from the hprc2 workdir,
+# so this step only redoes the netChainSubset -> chainInDel indel extraction.
+# Redmine #35415
+# Usage: hprc2XIndelsOne.sh <shortName> <hprc2Dir> <hprc2XDir>
+
+set -beEu -o pipefail
+# put the user build of chainInDel (with -t2bit support) ahead of the system copy
+export PATH=$HOME/bin/x86_64:/cluster/bin/x86_64:/cluster/bin/scripts:$PATH
+ulimit -s unlimited || true
+
+name="${1}"
+SRC="${2}"                 # existing hprc2 workdir (chain/, net/ reused)
+BED="${3}"                 # hprc2X workdir
+t2bit=/hive/data/genomes/hg38/hg38.2bit
+
+chainF="${SRC}/chain/${name}.chain"
+netF="${SRC}/net/${name}.net"
+mkdir -p "${BED}/arr"
+
+topChain="${BED}/arr/${name}.top.chain"
+netChainSubset "${netF}" "${chainF}" "${topChain}" -type=top 2>/dev/null
+$HOME/bin/x86_64/chainInDel -t2bit="${t2bit}" "${topChain}" "${name}" \
+  "${BED}/arr/${name}.indel.txt" 2>/dev/null
+rm -f "${topChain}"
+
+echo "OK ${name}"