ef61e73fc416622d8557ec2439df2344a1cc80c3
max
  Tue Jun 9 15:10:01 2026 -0700
lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv)

Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from
the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both
hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The
v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL
by parsimony-trimming REF/ALT and the net length change. The v2.0 build
recipe, converter and schema are kept but commented out in the makeDocs in
case wave-decomposed VCFs are released again, refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 1d4985a359c..6296dc37174 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -245,56 +245,56 @@
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC (placeholder)
     filterValues.svType DEL,INS,INSDEL
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:861080
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:22130
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:50
     filterByRange.AC on
     filterLabel.AC Allele Count (placeholder 50)
     skipEmptyFields on
 
-    track hprc2Sv
+    track hprc2v21Sv
     parent lrSv
-    bigDataUrl /gbdb/$D/lrSv/hprc2.bb
-    shortLabel HPRC v2 233 SVs
-    longLabel Structural Variants from the HPRC v2 Pangenome Graph (233 samples, minigraph-cactus)
+    bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb
+    shortLabel HPRC v2.1 233 SVs
+    longLabel Structural Variants from the HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus, raw deconstruct)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples
-    filterValues.svType INS,DEL,CPX,INV
+    filterValues.svType INS,DEL
     filterType.svType multipleListOr
     filterLabel.svType SV Type
-    filter.svLen 0:99113
+    filter.svLen 0:99835
     filterByRange.svLen on
     filterLabel.svLen SV Length
-    filter.insLen 0:97718
+    filter.insLen 0:1064897
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:463
     filterByRange.AC on
     filterLabel.AC Allele Count
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
-    filter.snarlLevel 0:10
+    filter.snarlLevel 0:7
     filterByRange.snarlLevel on
     filterLabel.snarlLevel Snarl Level
     skipEmptyFields on
 
     track hprc2JasmineSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb
     shortLabel HPRC2 Jasmine 231 SVs
     longLabel Structural Variants from 231 HPRC v2 Assemblies (14 SV Callers, Jasmine-merged; Hall Lab / Liao)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers)
     filterValues.svType DEL,INS
     filterType.svType multipleListOr