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/scripts/lrSv/lrSvHprc2Ro.as src/hg/makeDb/scripts/lrSv/lrSvHprc2Ro.as
new file mode 100644
index 00000000000..823ed168805
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvHprc2Ro.as
@@ -0,0 +1,21 @@
+table lrSvHprc2Ro
+"HPRC release-2.1 minigraph-cactus pangenome structural variants (233 samples)"
+    (
+    string chrom;           "Chromosome"
+    uint chromStart;        "Start position"
+    uint chromEnd;          "End position"
+    string name;            "Variant ID"
+    uint score;             "Score"
+    char[1] strand;         "Strand"
+    uint thickStart;        "Thick start (same as chromStart)"
+    uint thickEnd;          "Thick end (same as chromEnd)"
+    uint reserved;          "Item color"
+    string svType;          "SV Type|INS or DEL, classified from the net REF/ALT length change"
+    int svLen;              "SV Length|Length of the variant on the reference in base pairs"
+    int insLen;             "Insertion Length|Length of inserted sequence, 0 for DEL"
+    int AC;                 "Allele Count (AC)"
+    uint alleleNumber;      "Allele Number (AN)"
+    float alleleFreq;       "Allele Frequency (AF)"
+    uint nSamples;          "Samples with Data (NS)"
+    uint snarlLevel;        "Snarl Level|Nesting level in the pangenome snarl decomposition tree (0 = top level)"
+    )