7594507ca126d5242346787e42e13c52ea7709b1
max
  Fri Apr 17 08:40:31 2026 -0700
Add lrSv supertrack: long-read structural variants from 9 studies (hg38).

#Preview2 week - bugs introduced now will need a build patch to fix
Sub-tracks (all bigBed 9+):
han945Sv     - 945 Han Chinese, ONT (Gong 2025, PMID 39929826)
lrSv1kgOnt   - 1019 1000 Genomes, ONT, SVAN-annotated (Schloissnig 2025,
PMID 40702182; lifted from hs1)
tommoJpSv    - 333 Japanese (111 trios), ONT (Otsuki 2022, PMID 36127505)
aou1kSv      - 1027 All of Us, PacBio HiFi (Garimella 2025, PMID 41256123)
ga4kSv       - 502 GA4K pediatric rare disease, PacBio HiFi
(Cohen 2022, PMID 35305867)
decodeSv     - 3622 Icelanders, ONT (Beyter 2021, PMID 33972781)
hgsvc3Sv     - 65 HGSVC3 diverse haplotype-resolved assemblies, HiFi+ONT
(Logsdon 2025, PMID 40702183; merges insdel+inv tables)
kwanhoSv     - 100 post-mortem brains (PD/ILBD/HC), PacBio HiFi
(Kim 2026, PMID 41929179)
chirmade101Sv - 101 long-read WGS GWAS SVatalog cohort
(Chirmade 2026, PMID 41203876)

Includes per-track conversion scripts and autoSql under
scripts/lrSv/, the supertrack summary table in lrSv.html, and a
consolidated makeDoc at doc/hg38/lrSv.txt.

refs #36258

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/scripts/lrSv/lrSv.as src/hg/makeDb/scripts/lrSv/lrSv.as
new file mode 100644
index 00000000000..261a40aa7e0
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSv.as
@@ -0,0 +1,22 @@
+table lrSv
+"Long-read structural variants"
+    (
+    string chrom;       "Chromosome"
+    uint chromStart;    "Start position"
+    uint chromEnd;      "End position"
+    string name;        "Variant ID"
+    uint score;         "Score (quality)"
+    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, DUP, INV, or TRA"
+    int svLen;          "SV Length|Length of the structural variant in base pairs (absolute value)"
+    float alleleFreq;   "Allele Frequency|Fraction of samples carrying this variant"
+    uint sampleCount;   "Sample Count|Number of samples supporting this variant"
+    string ciPos;       "CI around Start|Confidence interval around start position"
+    string ciEnd;       "CI around End|Confidence interval around end position"
+    string chr2;        "Second Chromosome|Chromosome of second breakpoint (TRA only)"
+    string end2;        "Second Position|Position of second breakpoint (TRA only)"
+    lstring sampleList; "Supporting Samples|Comma-separated 1-based indices of supporting samples"
+    )