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/lrSvHgsvc3.as src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as
new file mode 100644
index 00000000000..00190f98798
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as
@@ -0,0 +1,26 @@
+table lrSvHgsvc3
+"HGSVC3 long-read structural variants (65 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|DEL, INS, or INV"
+    int svLen;               "SV Length|Absolute length of the SV in base pairs"
+    uint alleleCount;        "Allele Count|Number of haplotypes carrying the variant across 65 diploid samples"
+    uint sampleCount;        "Sample Count|Number of distinct samples carrying the variant (ignoring haplotype suffix)"
+    string homRef;           "Reference Homology|Homology (bp) at breakpoints in the reference (5',3'), insdel only"
+    string homTig;           "Contig Homology|Homology (bp) at breakpoints in the assembly contig (5',3'), insdel only"
+    string regionRefInner;   "Inversion Inner Region|Inner coordinate range of the inversion, INV only"
+    string te;               "Transposable Element|TE class of the inserted/deleted sequence, insdel only"
+    string refTrf;           "In Tandem Repeat|Variant falls in a reference Tandem Repeat Finder region (True/False)"
+    float refSd;             "Segmental Duplication Overlap|Fraction of the variant overlapping reference segmental duplications (0-1)"
+    lstring mergeSamples;    "Carrier Haplotypes|Comma-separated list of haplotype IDs carrying this variant"
+    string win500;           "Flanking +/- 500 bp|Genomic window around the variant"
+    string win2k;            "Flanking +/- 2000 bp|Genomic window around the variant"
+    )