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/hprc2XArrange.as src/hg/makeDb/scripts/hprc2X/hprc2XArrange.as
new file mode 100644
index 00000000000..8169c559da8
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2X/hprc2XArrange.as
@@ -0,0 +1,18 @@
+table hprc2Arrange
+"HPRC2 assembly rearrangements and indels relative to GRCh38"
+    (
+    string chrom;       "Chromosome (or contig, scaffold, etc.)"
+    uint   chromStart;  "Start position in chromosome"
+    uint   chromEnd;    "End position in chromosome"
+    string name;        "Name of item"
+    uint   score;       "Number of HPRC2 assemblies with this event"
+    char[1] strand;     "+ or -"
+    uint thickStart;    "Start of where display should be thick"
+    uint thickEnd;      "End of where display should be thick"
+    uint itemRgb;       "Color"
+    lstring source;     "List of assemblies with this event"
+    uint querySize;     "Size of item on assembly (query) side"
+    string label;       "Label for item"
+    uint size;          "Event size (bp)|Deletion/inversion/duplication: span on GRCh38. Insertion: bases inserted from the assembly."
+    lstring _mouseover; "mouseOver for item"
+    )