f058c8fe4601b223ff47468eb3525c05ccd03850
max
  Wed Apr 22 09:17:17 2026 -0700
srSv: new short-read SV supertrack, split out of lrSv

Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr,
tommoJpCnv) out of the Long-read SV supertrack into a new sibling
supertrack srSv (Short-read SVs), so the lrSv collection contains
only long-read callsets. Filter fields (svType, svLen, insLen, AC)
are mirrored at the srSv supertrack level to keep the UX parallel
to lrSv.

- trackDb: new human/srSv.ra with the three subtrack stanzas and
updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas
removed from human/lrSv.ra. human/trackDb.ra now includes
srSv.ra. Also a new human/srSv.html overview page; the SR rows
and SR-specific paragraphs removed from human/lrSv.html.
- Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/
{lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to
scripts/srSv/ with git mv (history preserved) and renamed to
drop the "lrSv" prefix. Internal path references in abelSvBuild.sh
and abelSvVcfToBed.py updated.
- makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and
extended with the onekg3202Sr and tommoJpCnv sections moved from
lrSv.txt. lrSv.txt leaves a pointer.
- Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr,
lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*.
/gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and
/gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/.

refs #36258

diff --git src/hg/makeDb/trackDb/human/srSv.html src/hg/makeDb/trackDb/human/srSv.html
new file mode 100644
index 00000000000..252ace3e465
--- /dev/null
+++ src/hg/makeDb/trackDb/human/srSv.html
@@ -0,0 +1,105 @@
+<h2>Description</h2>
+<p>
+This track collection contains structural variant (SV) and copy-number variant
+(CNV) callsets derived from Illumina <b>short-read</b> sequencing. Most SV
+tracks in the browser now come from long-read platforms (see the companion
+<a href="hgTrackUi?g=lrSv">Long-read SVs</a> supertrack); the short-read
+callsets here are included as comparators so users can evaluate the extra
+sensitivity of long-read calls and cross-check a variant across technologies.
+</p>
+
+<h3>Available Datasets</h3>
+<p>
+SV length statistics (min / median / max) are computed from the <tt>svLen</tt>
+field of each track, in base pairs. For the Abel CCDG callset, a large
+fraction of records are breakend (BND) translocations where <tt>svLen=-1</tt>
+is used as a sentinel, which shows up in both min and median.
+</p>
+<table class="stdTbl">
+<tr>
+  <th>Dataset</th>
+  <th>N samples</th>
+  <th>Cohort / disease</th>
+  <th>Sequencing</th>
+  <th>SVs</th>
+  <th>Min</th>
+  <th>Median</th>
+  <th>Max</th>
+</tr>
+<tr>
+  <td><a href="hgTrackUi?g=abelSv">CCDG 17,795</a></td>
+  <td>17,795</td>
+  <td>NHGRI CCDG + PAGE + SGDP (B38 native + B37 lifted)</td>
+  <td>Illumina short-read (LUMPY + CNVnator + svtyper)</td>
+  <td>737,998</td>
+  <td>-1</td>
+  <td>-1</td>
+  <td>217,985,413</td>
+</tr>
+<tr>
+  <td><a href="hgTrackUi?g=onekg3202Sr">1KG 3202</a></td>
+  <td>3,202</td>
+  <td>1000 Genomes expanded cohort</td>
+  <td>Illumina short-read (GATK-SV)</td>
+  <td>173,366</td>
+  <td>1</td>
+  <td>314</td>
+  <td>154,807,729</td>
+</tr>
+<tr>
+  <td><a href="hgTrackUi?g=tommoJpCnv">ToMMo 48K CNV</a></td>
+  <td>48,874</td>
+  <td>Japanese, general population</td>
+  <td>Illumina short-read (GATK CNV, 1 kb bins, shown as two bigWigs)</td>
+  <td colspan="4">~2M bins with CNV carriers; not comparable to per-SV counts above</td>
+</tr>
+</table>
+
+<h3>CCDG 17,795 SVs (<a href="hgTrackUi?g=abelSv">abelSv</a>)</h3>
+<p>
+Site-frequency callset from 17,795 deeply sequenced genomes (Abel et al. 2020,
+Nature; PMID 32460305). Two non-overlapping public releases are combined in
+this track: the B38 callset (14,623 samples called natively on GRCh38) and the
+B37 callset (8,417 samples, lifted). Variants are colored by SV type
+(DEL / DUP / INV / MEI / BND) and carry per-population allele counts for eight
+ancestry groups plus a HIGH/LOW confidence filter.
+</p>
+
+<h3>1KG 3202 SVs (<a href="hgTrackUi?g=onekg3202Sr">onekg3202Sr</a>)</h3>
+<p>
+1000 Genomes 3202-sample Illumina short-read GATK-SV callset (Byrska-Bishop
+et al. 2022). 173,366 SVs across 7 classes (DEL, INS, DUP, INV, CPX, CNV,
+CTX) with AC/AN/AF and per-superpopulation AFs (AFR/AMR/ASN/EUR/SAN).
+</p>
+
+<h3>ToMMo 48K CNV SR (<a href="hgTrackUi?g=tommoJpCnv">tommoJpCnv</a>)</h3>
+<p>
+Per-1 kb-bin copy-number carrier counts from short-read whole-genome
+sequencing of 48,874 Japanese individuals (jMorp 48KJPN-CNV Frequency Panel,
+release 20230828), called with GATK CNV germline workflows. Shown as a
+multiWig overlay: red = samples with copy-number loss (CN&lt;2) per bin,
+green = samples with gain (CN&gt;2) per bin. This is a useful short-read
+point of comparison to the ToMMo 333-sample long-read SV track under the
+Long-read SVs supertrack.
+</p>
+
+<h2>Data Access</h2>
+<p>
+See the Data Access section of each subtrack's page for download links.
+Build documentation lives alongside the scripts at
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/srSv.txt" target="_blank">
+doc/hg38/srSv.txt</a>; conversion scripts and autoSql schemas are at
+<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/srSv" target="_blank">
+makeDb/scripts/srSv</a>.
+</p>
+
+<h2>Credits</h2>
+<p>
+Each subtrack credits its respective upstream project; see the individual
+description pages.
+</p>
+
+<h2>References</h2>
+<p>
+See the individual subtrack description pages for the specific references.
+</p>