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/lrSvChirmade101.as src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as
new file mode 100644
index 00000000000..fcfa10edcde
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as
@@ -0,0 +1,46 @@
+table lrSvChirmade101
+"Chirmade 2026 (GWAS SVatalog) long-read structural variants"
+    (
+    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, dup, inv, or complex"
+    int svLen;                 "SV Length|Absolute length of the SV in base pairs"
+    uint gcPct;                "GC Content|Percent GC in the SV region"
+    string cytoband;           "Cytoband"
+    uint geneCount;            "Gene Count|Number of genes overlapping the SV"
+    lstring geneNames;         "Overlapping Genes|Comma-separated gene symbols"
+    string geneAtStart;        "Gene at Start|Gene at the left breakpoint"
+    string geneAtEnd;          "Gene at End|Gene at the right breakpoint"
+    lstring exonName;          "Overlapping Exons"
+    lstring cdsName;           "Overlapping CDS"
+    string darkOverlap;        "Dark Genes Overlap|Percent overlap with 'dark' (low-mappability) genes"
+    lstring clinGenHi;         "ClinGen Haploinsufficient|Haploinsufficiency score/evidence per gene"
+    lstring clinGenTs;         "ClinGen Triplosensitive|Triplosensitivity score/evidence per gene"
+    lstring gnomadLoefUpper;   "gnomAD LOEUF|Observed/expected LoF upper bound per gene"
+    lstring gnomadMisUpper;    "gnomAD Mis O/E|Observed/expected missense upper bound per gene"
+    lstring gnomadPli;         "gnomAD pLI|Per-gene pLI"
+    lstring gnomadPrec;        "gnomAD pRec|Per-gene pRec"
+    string repeatPct;          "Repeat Overlap|Percent overlap with repetitive regions"
+    string dirtyPct;           "Dirty Region Overlap|Percent overlap with 'dirty' / low-quality regions"
+    lstring chrRegion;         "Chromosome Region"
+    lstring cgd;               "CGD|Clinical Genomic Database gene annotation"
+    lstring omimPheno;         "OMIM Phenotype"
+    lstring omimInh;           "OMIM Inheritance"
+    lstring clinGenRegion;     "ClinGen Region"
+    lstring decipherRegion;    "Decipher Region"
+    lstring clinvarVarId;      "ClinVar Variant ID"
+    string gnomadAfMax;        "gnomAD AF Max (90% RO)|Max allele frequency across gnomAD populations for overlapping SV"
+    string gnomadPopAfMax;     "gnomAD Population AF Max"
+    string gnomadHomRefFreq;   "gnomAD Hom/Ref Freq"
+    string gnomadHetFreq;      "gnomAD Het Freq"
+    string gnomadHomAltFreq;   "gnomAD Hom/Alt Freq"
+    string dgvPct;             "DGV Overlap|Percent overlap with Database of Genomic Variants"
+    string dgv50ro;            "DGV 50% RO|Matched DGV variant at >=50% reciprocal overlap"
+    )