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/lrSvTommoJp.as src/hg/makeDb/scripts/lrSv/lrSvTommoJp.as
new file mode 100644
index 00000000000..41b6fb94c0a
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvTommoJp.as
@@ -0,0 +1,21 @@
+table lrSvTommoJp
+"ToMMo Japanese long-read structural variants"
+    (
+    string chrom;           "Chromosome"
+    uint chromStart;        "Start position"
+    uint chromEnd;          "End position"
+    string name;            "Variant Name"
+    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 or INS"
+    int svLen;              "SV Length|Length of the structural variant in base pairs"
+    float alleleFreq;       "Allele Frequency|Fraction of alleles carrying this variant (AF field)"
+    uint alleleCount;       "Allele Count|Number of alleles carrying this variant"
+    uint alleleNumber;      "Allele Number|Total number of alleles genotyped"
+    float errFamilyRatio;   "Mendelian Error Rate|Fraction of families showing Mendelian inheritance errors"
+    uint errFamilyNum;      "Families with Errors|Number of families with Mendelian errors"
+    uint familyNum;         "Families Genotyped|Number of families without missing calls"
+    )