95208355e2c667d194b29ee78c8ca8a09c2c2596
max
  Fri Jul 17 08:51:28 2026 -0700
lrSv: add NIH CARD long-read SV subtrack (cardSv)

#Preview2 week - bugs introduced now will need a build patch to fix
Add the NIH CARD Long-Read Initiative structural-variant catalogue (351
post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC
African/African-admixed) as a new subtrack of the Long-read SVs container.
The provider bigBed is re-derived into the shared lrSv schema: signed svLen
made positive (reference span), an explicit insLen added, the single
DUP:TANDEM folded to DUP, and colors remapped to the container's shared
svColor() palette. All 228,855 provider records are carried through 1:1.
Adds the converter and autoSql, the trackDb stanza with filters consistent
with the sibling subtracks, a full description page, a summary row and blurb
on the container page, and a makeDoc section. refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSvCard.as src/hg/makeDb/scripts/lrSv/lrSvCard.as
new file mode 100644
index 00000000000..fcde2f4c613
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvCard.as
@@ -0,0 +1,20 @@
+table lrSvCard
+"NIH CARD long-read structural variants (351 brain samples: 205 NABEC, 146 HBCC)"
+    (
+    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|DEL, INS, INV or DUP"
+    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/INV/DUP"
+    int AC;                 "Allele Count|Number of samples carrying this variant (genotyped carrier count)"
+    float alleleFreq;       "Allele Frequency|Fraction of samples carrying this variant (source VCF AF)"
+    uint nabecCount;        "NABEC Carriers|Carrier samples of European ancestry (NABEC cohort)"
+    uint hbccCount;         "HBCC Carriers|Carrier samples of African/African-admixed ancestry (HBCC cohort)"
+    )