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/lrSvAou1k.as src/hg/makeDb/scripts/lrSv/lrSvAou1k.as
new file mode 100644
index 00000000000..beb1cf957ee
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvAou1k.as
@@ -0,0 +1,33 @@
+table lrSvAou1k
+"All of Us long-read structural variants"
+    (
+    string chrom;           "Chromosome"
+    uint chromStart;        "Start position"
+    uint chromEnd;          "End position"
+    string name;            "Variant Name"
+    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 or INS"
+    int svLen;              "SV Length|Length of the structural variant in base pairs"
+    float afAfr;            "AF African|Allele frequency in African/African American samples"
+    float afAmr;            "AF Admixed American|Allele frequency in Admixed American samples"
+    float afEas;            "AF East Asian|Allele frequency in East Asian samples"
+    float afEur;            "AF European|Allele frequency in European samples"
+    float afSas;            "AF South Asian|Allele frequency in South Asian samples"
+    string fst;             "Fst (AFR vs Non-AFR)|Fixation index between African and non-African populations"
+    lstring omimGenes;      "OMIM Genes|OMIM genes intersected with pLI and LOEUF scores"
+    lstring diseaseGenes;   "Disease Genes|Disease genes intersected with pLI and LOEUF scores"
+    lstring cancerGenes;    "Cancer Genes|Cancer genes intersected with pLI and LOEUF scores"
+    lstring acmgGenes;      "ACMG Genes|ACMG genes intersected with pLI and LOEUF scores"
+    string regElement;      "Regulatory Element|Type of regulatory element intersected (e.g. enhancer, promoter)"
+    string segDup;          "SegDup|Segmental duplication association (INS: within 1kb, DEL: intersect)"
+    string tandemRepeat;    "Tandem Repeat|Tandem repeat intersected"
+    string otherLrDatasets; "Other LR Datasets|Detected in other long-read datasets (HPRC, HGSVC, 1KG-ONT)"
+    string detectedInSr;    "Detected in SR|Detected in matched AoU short-read data"
+    lstring eqtls;          "eQTLs|eQTL associations: gene(qvalue)"
+    lstring gwas;           "GWAS Associations|GWAS associations: trait(gene, rsID, pvalue, LD_r2)"
+    lstring traitAssoc;     "SV-Trait Associations|SV-trait associations in AoU Phase I (Carrier%, Non-carrier%, OR, 95% CI, pvalue)"
+    )