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/lrSvKwanho.as src/hg/makeDb/scripts/lrSv/lrSvKwanho.as
new file mode 100644
index 00000000000..8a490015eb6
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvKwanho.as
@@ -0,0 +1,42 @@
+table lrSvKwanho
+"Kim 2026 Parkinson's disease brain 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 or INV"
+    int svLen;                  "SV Length|Absolute length of the SV in base pairs"
+    string sizeBin;             "Size Bin|Length category used in the paper (e.g. [50,100))"
+    uint qual;                  "Quality|Variant quality score from the joint callset"
+    uint supp;                  "Caller Support|Number of SV callers supporting this variant"
+    string suppVec;             "Cohort Support Vector|Bitmask indicating which cohorts carry the variant (PD/ILBD/HC)"
+    float missingRate;          "Missing-genotype Rate|Fraction of samples with missing genotype at this site"
+    float caseRate;             "Case Carrier Rate|Fraction of PD+ILBD cases carrying the variant"
+    float controlRate;          "Control Carrier Rate|Fraction of HC controls carrying the variant"
+    float differentialRate;     "Case-Control Differential|caseRate - controlRate (negative: enriched in controls)"
+    float afPd;                 "Allele Frequency (PD)|Alternate allele frequency in Parkinson's disease samples"
+    float afHc;                 "Allele Frequency (HC)|Alternate allele frequency in healthy-control samples"
+    float afIlbd;               "Allele Frequency (ILBD)|Alternate allele frequency in incidental Lewy body disease samples"
+    uint acPd;                  "Allele Count (PD)|Alternate allele count in PD samples"
+    uint acHc;                  "Allele Count (HC)|Alternate allele count in HC samples"
+    uint acIlbd;                "Allele Count (ILBD)|Alternate allele count in ILBD samples"
+    uint anPd;                  "Allele Number (PD)|Total called alleles in PD samples"
+    uint anHc;                  "Allele Number (HC)|Total called alleles in HC samples"
+    uint anIlbd;                "Allele Number (ILBD)|Total called alleles in ILBD samples"
+    uint nCarriersPd;           "Carrier Count (PD)"
+    uint nCarriersHc;           "Carrier Count (HC)"
+    uint nCarriersIlbd;         "Carrier Count (ILBD)"
+    uint ldSnpsCount;           "LD SNPs|Number of nearby SNPs in linkage disequilibrium with this SV"
+    uint totalSnpsNearby;       "Nearby SNPs|Total number of SNPs in the surrounding window"
+    float avgMapQuality;        "Avg Mapping Quality|Average read mapping quality at the SV"
+    float avgReadsPerSample;    "Avg Reads / Sample|Average supporting reads per sample"
+    lstring pdCarriers;         "PD Carriers|Sample IDs of PD carriers"
+    lstring hcCarriers;         "HC Carriers|Sample IDs of HC carriers"
+    lstring ilbdCarriers;       "ILBD Carriers|Sample IDs of ILBD carriers"
+    )