526213b2893134217a300ff913e11b4e98d67991
max
  Mon Apr 20 08:50:10 2026 -0700
lrSv: add cpc1Sv and aprSv pangenome SV subtracks (hg38, hs1)

cpc1Sv: 97,205 SVs from the CPC + HPRC Phase 1 pangenome (Gao et al 2023,
Nature; PMID 37316654) built on T2T-CHM13v2, with 53 Chinese and 47 HPRC
samples. Each graph snarl site is shown as one item with alt alleles
classified by length delta (INS/DEL/CPX, 50 bp threshold) and collapsed.

aprSv: 103,077 SVs from the Arabic Pangenome Reference (Nassir et al.
2025, Nat Commun; PMID 40707445) built on T2T-CHM13v2 from 53 UAE-resident
Arab individuals. Same multi-allele classification as cpc1Sv, with alt
alleles iterated within each multi-allelic row.

Both tracks load natively on hs1 and are lifted to hg38 with
hs1ToHg38.over.chain.gz.

refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSvCpc1.as src/hg/makeDb/scripts/lrSv/lrSvCpc1.as
new file mode 100644
index 00000000000..1cb2ee7ff19
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvCpc1.as
@@ -0,0 +1,20 @@
+table lrSvCpc1
+"CPC+HPRC Phase 1 pangenome structural variants, collapsed by graph snarl site"
+    (
+    string chrom;        "Chromosome"
+    uint   chromStart;   "Start position"
+    uint   chromEnd;     "End position"
+    string name;         "Graph snarl ID (variant site)"
+    uint   score;        "Score, 0-1000 (scaled AF)"
+    char[1] strand;      "Strand (.)"
+    uint   thickStart;   "Thick start"
+    uint   thickEnd;     "Thick end"
+    uint   itemRgb;      "Color by SV type"
+    string svType;       "SV Type|INS, DEL, CPX or MIXED (MIXED = snarl with alts of different classes)"
+    int    svLen;        "SV Length|max |len(ALT) - len(REF)| across alt alleles"
+    int    numAlts;      "Number of alt alleles|collapsed into this snarl"
+    int    alleleCount;  "Allele Count (AC)|sum across all alt alleles at this site"
+    int    alleleNumber; "Allele Number (AN)|called alleles at this site"
+    float  alleleFreq;   "Allele Frequency (AF)|alleleCount / alleleNumber"
+    int    numSamples;   "Samples with data (NS)|number of samples with at least one called allele"
+    )