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/runSamples.sh src/hg/makeDb/scripts/hprc2X/runSamples.sh
new file mode 100755
index 00000000000..1d357390ff4
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2X/runSamples.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+set -beEu -o pipefail
+D=/hive/data/genomes/hg38/bed/hprc2X
+for i in 1 2 3 4 5; do
+  bash $D/buildSample.sh $D/samp$i 88 "samp$i" >> $D/samples.build.log 2>&1
+  bash $D/dbsnpStats.sh $D/samp$i.canon.tsv 88 "rel2samp$i"
+done
+echo "ALLDONE"