9a11061ca6b40fe16bdfd09b1af53192f6c7c85b
max
  Tue Apr 21 08:13:02 2026 -0700
lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3

Subtrack stanzas for these SV callsets landed in earlier commits but
the conversion scripts and per-track HTML description pages were
never added; trackDb therefore had no doc to serve. This commit
catches up.

Docs (new):
- colorsDbSv.html     CoLoRSdb 1,427-sample long-read SVs
- gustafsonSv.html    1KG ONT 100 (Gustafson 2024, PMID 39358015)
- hgsvc2Sv.html       HGSVC2 (Ebert 2021, PMID 33632895)
- hprc2Sv.html        HPRC release-2 pangenome SVs (no PMID yet;
see humanpangenome.org/hprc-data-release-2/)
- onekg3202Sr.html    1KG 3202 Illumina SHORT-READ GATK-SV
(Byrska-Bishop 2022, PMID 36055201)

Scripts (new):
- lrSvGustafson.as / lrSvGustafsonVcfToBed.py
- lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py  (merges insdel + inv tables)
- lrSvHprc2.as / lrSvHprc2VcfToBed.py    (streams wave-decomposed VCF,
explodes multi-allelic rows,
filters to SV-sized or INV)
- lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py

HGSVC3 also on hs1:
- hgsvc3Sv.html: note that the hs1 build is native (not lifted):
HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and
released separate annotation tables per reference. Added the
T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb
download link to Data Access.
- doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers
back to doc/hg38/lrSv.txt for the full process.

refs #36258

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/scripts/lrSv/lrSv1kg3202Sr.as src/hg/makeDb/scripts/lrSv/lrSv1kg3202Sr.as
new file mode 100644
index 00000000000..53dff9d8a37
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSv1kg3202Sr.as
@@ -0,0 +1,30 @@
+table lrSv1kg3202Sr
+"1000 Genomes 3202-sample short-read GATK-SV structural variants (Byrska-Bishop 2022)"
+    (
+    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, CPX, CTX or CNV"
+    int svLen;              "SV Length|Absolute length of the SV in base pairs"
+    uint alleleCount;       "Allele Count (AC)"
+    uint alleleNumber;      "Allele Number (AN)"
+    float alleleFreq;       "Allele Frequency (AF)"
+    float popmaxAf;         "Population Max AF|Highest AF across the five superpopulations"
+    float afAfr;            "AF African"
+    float afAmr;            "AF Admixed American"
+    float afAsn;            "AF East Asian"
+    float afEur;            "AF European"
+    float afSan;            "AF South Asian"
+    uint nHet;              "Het Carriers|Number of heterozygous samples"
+    uint nHomalt;           "Hom-alt Carriers|Number of homozygous-alternate samples"
+    string algorithms;      "Source Algorithms|SV callers contributing evidence (depth, PE, SR, ...)"
+    string source;          "Source Pipeline|Upstream SV pipeline (gatksv, svtools, etc.)"
+    string filterStatus;    "Filter Status|PASS, LowQual, MinGQ, etc. (VCF FILTER column)"
+    string chr2;            "Second Chromosome|For translocations (CTX)"
+    )