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/trackDb/human/onekg3202Sr.html src/hg/makeDb/trackDb/human/onekg3202Sr.html
new file mode 100644
index 00000000000..b0bc17186ad
--- /dev/null
+++ src/hg/makeDb/trackDb/human/onekg3202Sr.html
@@ -0,0 +1,112 @@
+<h2>Description</h2>
+<p>
+<b>This track is the only short-read dataset in the Long-Read Variants
+track collection; it is included for comparison with the long-read
+callsets.</b>
+</p>
+<p>
+This track shows structural variants (SVs) from the expanded 1000 Genomes
+Project cohort of 3,202 high-coverage <b>Illumina short-read</b>
+whole-genome sequences (including 602 trios), sequenced at ~30x on NovaSeq
+6000 and described in Byrska-Bishop et al. 2022. SVs were called with the
+GATK-SV / svtools integrated pipeline; this release adds re-genotyped
+novel insertions and recomputed allele frequencies per continental group.
+</p>
+<p>
+The track contains 173,366 SVs across seven classes: 90,259 deletions
+(DEL), 49,693 insertions (INS), 28,242 duplications (DUP), 3,568 complex
+events (CPX), 920 inversions (INV), 673 multi-allelic copy-number variants
+(CNV) and 11 reciprocal translocations (CTX). Allele counts, allele
+frequencies and per-superpopulation frequencies (AFR, AMR, EAS/ASN, EUR,
+SAS/SAN) are provided for each site.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+Items are colored by SV type:
+<ul>
+<li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li>
+<li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li>
+<li><span style="color: rgb(0,160,0);">Duplications (DUP)</span> - green</li>
+<li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li>
+<li><span style="color: rgb(140,0,200);">Complex (CPX)</span> - purple</li>
+<li><span style="color: rgb(150,80,0);">Copy-number variants (CNV)</span> - brown</li>
+<li><span style="color: rgb(100,100,100);">Translocations (CTX)</span> - grey</li>
+</ul>
+</p>
+<p>
+Insertions are placed at the insertion site; deletions, duplications,
+inversions, complex and copy-number variants span the affected reference
+interval. Translocations show only the chr1-side breakpoint; the partner
+chromosome is reported on the detail page.
+</p>
+<p>
+Filters are available for SV type, SV length, overall allele frequency,
+population-max allele frequency and per-population AFs (African and
+European). The detail page also shows heterozygous / homozygous-alternate
+carrier counts, the set of upstream SV callers, the upstream pipeline
+source and the VCF FILTER status.
+</p>
+
+<h2>Methods</h2>
+<p>
+The 1000 Genomes expanded cohort was sequenced on Illumina NovaSeq 6000
+at ~30x coverage with 2x150 bp reads. Structural variants were called
+with the GATK-SV cohort pipeline and merged with svtools; novel insertions
+were re-genotyped to produce the integrated callset used here
+(<tt>1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz</tt>).
+Allele frequencies were computed genome-wide and per-population
+(AFR, AMR, EAS/ASN, EUR, SAS/SAN).
+</p>
+<p>
+<b>Why a short-read track in a long-read collection?</b> Short-read SV
+callsets such as this one generally have high precision for deletions
+and duplications but miss many insertions, repeat expansions and
+variants in complex/low-mappability regions that long-read technologies
+can resolve. Displaying this callset alongside the long-read tracks in
+this collection makes it easier to spot variants that are unique to
+long-read data or that have substantially different breakpoints when
+called from short reads.
+</p>
+
+<h2>Data Access</h2>
+<p>
+The data can be explored interactively in table format with the
+<a href="../cgi-bin/hgTables">Table Browser</a> or the
+<a href="../cgi-bin/hgIntegrator">Data Integrator</a>, and accessed
+programmatically through our <a href="https://api.genome.ucsc.edu">API</a>,
+track=<i>onekg3202Sr</i>.
+</p>
+<p>
+The bigBed is available from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our
+download server</a> as <tt>onekg3202sr.bb</tt>. Example:
+<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/onekg3202sr.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>.
+</p>
+<p>
+The original joint-genotyped VCF is available from the
+<a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/" target="_blank">
+IGSR 1000 Genomes Illumina SV integration folder</a>.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to Byrska-Bishop, Marth and the 1000 Genomes / NYGC team for
+releasing this dataset, and to the GATK-SV developers for the cohort
+calling pipeline.
+</p>
+
+<h2>References</h2>
+
+
+<p>
+Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R,
+Nagulapalli K <em>et al</em>.
+<a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)00991-6" target="_blank">
+High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602
+trios</a>.
+<em>Cell</em>. 2022 Sep 1;185(18):3426-3440.e19.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36055201" target="_blank">36055201</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9439720/" target="_blank">PMC9439720</a>
+</p>
+