9a63ecfed718d4ad0b2c5212c7ad8844c9d23531
lrnassar
  Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258

Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).

diff --git src/hg/makeDb/trackDb/human/han945Sv.html src/hg/makeDb/trackDb/human/han945Sv.html
index a719ff0018a..00a85165dab 100644
--- src/hg/makeDb/trackDb/human/han945Sv.html
+++ src/hg/makeDb/trackDb/human/han945Sv.html
@@ -1,90 +1,90 @@
 <h2>Description</h2>
 <p>
 This track shows structural variants (SVs) identified by long-read sequencing
 of 945 Han Chinese individuals. The dataset contains 111,288 SVs merged across
 samples using SURVIVOR, including 49,518 deletions, 42,300 insertions,
 13,503 duplications, 5,595 inversions, and 372 translocations.
 </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);">Translocations (TRA)</span> - purple</li>
 </ul>
 </p>
 <p>
 Filters are available for SV type, SV length, allele frequency, and number of
 supporting samples. For insertions, the item is placed at the insertion site
 with a width of 1 bp. For translocations, only the first breakpoint is shown;
 the second breakpoint chromosome and position are listed in the item details.
 </p>
 
 <h2>Methods</h2>
 <p>
 Gong et al. 2025 performed Oxford Nanopore long-read sequencing of 945
 Han Chinese individuals on PromethION instruments with R9.4 flow cells.
 Reads were aligned to GRCh38.p13 with NGMLR v0.2.7 using ONT-tuned
 parameters, and a joint-calling strategy was used to call SVs at moderate
 coverage: per-sample discovery with
 <a href="https://github.com/tjiangHIT/cuteSV" target="_blank">cuteSV</a>
 v1.0.13, merging of breakpoints within 500 bp across individuals with
 <a href="https://github.com/fritzsedlazeck/SURVIVOR" target="_blank">SURVIVOR</a>
 v1.0.6, per-sample re-genotyping of the merged set with LRcaller v1.0, and
 a final BCFtools merge. SVs in centromeric, pericentromeric and gap regions
 were filtered out, yielding 111,288 high-quality SVs: 49,518 deletions,
 42,300 insertions, 13,503 duplications, 5,595 inversions and 372
 translocations.
 </p>
 <p>
 The site-only VCF released at
 <a href="https://www.biosino.org/node/analysis/detail/OEZ007028" target="_blank">
 OMIX accession OED00945268</a> (<tt>OED00945268_Han_945samples_SV.vcf.gz</tt>)
 was converted to BED for this track.
 </p>
 <p>
 The step-by-step build commands (download, format conversion, bigBed build)
 are recorded in the UCSC makeDoc for this track container:
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank">
 doc/hg38/lrSv.txt</a>. The conversion scripts and autoSql schemas live in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank">
-makeDb/scripts/lrSv</a>.
+makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSv.ra" target="_blank">trackDb/human/lrSv.ra</a>.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The raw VCF data was obtained from the
 <a href="https://www.biosino.org/node/analysis/detail/OEZ007028" target="_blank">OMIX</a>
 repository (accession OED00945268) at the National Genomics Data Center (NGDC),
 China National Center for Bioinformation.
 </p>
 <p>
 The source VCF also encodes phased per-sample genotypes: the <tt>sampleList</tt>
 field on the detail page is derived from the SURVIVOR <tt>SUPP_VEC</tt> bitmask
 and is an ordered list of the 1-based indices of the 945 samples carrying
 each SV. The full per-sample phased VCF can be browsed as a separate track in
 the <a href="hgTrackUi?g=han945SvVcf">SVs from 945 Han Chinese</a> entry of
 the <a href="hgTrackUi?g=phasedVars">Phased Variants</a> track collection.
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to Gong et al. for making their structural variant calls publicly available.
 </p>
 
 <h2>References</h2>
 
 <p>
 Gong J, Sun H, Wang K, Zhao Y, Huang Y, Chen Q, Qiao H, Gao Y, Zhao J, Ling Y <em>et al</em>.
 <a href="https://doi.org/10.1038/s41467-025-56661-9" target="_blank">
 Long-read sequencing of 945 Han individuals identifies structural variants associated with
 phenotypic diversity and disease susceptibility</a>.
 <em>Nat Commun</em>. 2025 Feb 10;16(1):1494.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39929826" target="_blank">39929826</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811171/" target="_blank">PMC11811171</a>
 </p>