e11e10c01c975653b7f0102601cabd52967d2c80 max Fri Aug 14 05:58:23 2026 -0700 lrSv: author-provided noyvertSv description, Vienna ONT naming, hs1 Lin update, refs #38099 - noyvertSv.html: replace the Description with the author-provided text (imputation purpose, singletons excluded, subset-of-Vienna relationship) - rename "1KG ONT Vienna" -> "1KG Vienna ONT" to match the subtrack and merged-track labels (noyvertSv.html and the hs1 lrSv page) - hs1 lrSv page: add the 1KG Lin merged subtrack (now native on T2T-CHM13, 614,522 SVs) and reorder the summary table and detail sections to match the track (priority) order - lrSv1kLin.html: link the source Lin et al. dataset on GitHub diff --git src/hg/makeDb/trackDb/human/hs1/html/lrSv.html src/hg/makeDb/trackDb/human/hs1/html/lrSv.html index 3f3a28ece6e..5ddacee7dd7 100644 --- src/hg/makeDb/trackDb/human/hs1/html/lrSv.html +++ src/hg/makeDb/trackDb/human/hs1/html/lrSv.html @@ -4,96 +4,108 @@ sequencing, called natively against the T2T-CHM13 reference (hs1). It is the T2T-CHM13 companion to the GRCh38 Long-read SVs collection. </p> <p> Only a subset of the long-read SV datasets have been released with native T2T-CHM13 coordinates, and those are the subtracks shown here. The remaining cohorts in the collection were released on GRCh38 only. For the full set of datasets, see the <a href="../cgi-bin/hgTrackUi?db=hg38&g=longReadVariants">hg38 Long-read SVs</a> track. </p> <h2>Available datasets (T2T-CHM13 native)</h2> <table class="stdTbl"> <tr><th>Dataset</th><th>N samples</th><th>Technology</th><th>SV count (hs1)</th></tr> <tr><td><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb</a></td><td>1,427</td><td>PacBio HiFi</td><td>839,714</td></tr> -<tr><td><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a></td><td>1,019</td><td>ONT</td><td>161,332</td></tr> -<tr><td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td><td>65</td><td>HiFi + ONT</td><td>188,500</td></tr> +<tr><td><a href="hgTrackUi?g=lrSv1kLin">1KG Lin merged</a></td><td>1,218</td><td>ONT + assembly (merged)</td><td>614,522</td></tr> +<tr><td><a href="hgTrackUi?g=lrSv1kgOnt">1KG Vienna ONT</a></td><td>1,019</td><td>ONT</td><td>161,332</td></tr> <tr><td><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1</a></td><td>233</td><td>Pangenome (minigraph-cactus)</td><td>541,176</td></tr> -<tr><td><a href="hgTrackUi?g=aprSv">Arab APR</a></td><td>53</td><td>HiFi + ONT pangenome</td><td>103,077</td></tr> +<tr><td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td><td>65</td><td>HiFi + ONT</td><td>188,500</td></tr> <tr><td><a href="hgTrackUi?g=cpc1Sv">CPC</a></td><td>58</td><td>HiFi pangenome</td><td>46,092</td></tr> +<tr><td><a href="hgTrackUi?g=aprSv">Arab APR</a></td><td>53</td><td>HiFi + ONT pangenome</td><td>103,077</td></tr> </table> <p> HGSVC3 and HPRC v2.1 are built directly from the consortia's T2T-CHM13 -releases; CoLoRSdb, 1KG ONT Vienna, Arab APR, and CPC are built from callsets -or pangenome graphs native to T2T-CHM13. Per-subtrack details, cohorts, and -citations are on each subtrack's own description page. +releases; CoLoRSdb, 1KG Lin merged, 1KG Vienna ONT, Arab APR, and CPC are built +from callsets or pangenome graphs native to T2T-CHM13. Per-subtrack details, +cohorts, and citations are on each subtrack's own description page. </p> <h3><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb SVs</a></h3> <p> Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. ~840k SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort. </p> -<h3><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna SVs</a></h3> +<h3><a href="hgTrackUi?g=lrSv1kLin">1KG Lin merged SVs</a></h3> +<p> +A merged long-read SV callset spanning 1,218 individuals of the 1000 Genomes +Project (Lin et al.), combining 293 near-T2T haplotype-resolved assemblies +(HPRC and HGSVC), 480 University of Washington Oxford Nanopore genomes, and 445 +Vienna Oxford Nanopore genomes. Structural variants were discovered with ten +long-read callers, and the BoostSV machine-learning tool selected the best +allele to represent each SV across platforms and coverages. ~615k SVs +(insertions and deletions) in native T2T-CHM13 coordinates. +</p> + +<h3><a href="hgTrackUi?g=lrSv1kgOnt">1KG Vienna ONT SVs</a></h3> <p> Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT), called natively against T2T-CHM13. ~161k SVs annotated with SVAN, classifying insertions and deletions by mechanism of origin (mobile elements, VNTRs, processed pseudogenes, and others). </p> +<h3><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1 SVs</a></h3> +<p> +Structural variants derived from the Human Pangenome Reference Consortium +release-2.1 minigraph-cactus pangenome graph, built from 233 PacBio HiFi +haplotype-resolved assemblies. ~541k SV-sized alleles (insertions and +deletions) extracted from the T2T-CHM13 graph with vg deconstruct. +</p> + <h3><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3 SVs</a></h3> <p> Structural variants from 65 diverse individuals sequenced and de novo assembled by the Human Genome Structural Variation Consortium phase 3 (HGSVC3), from the consortium's native T2T-CHM13 annotation tables. ~189k haplotype-resolved SVs (deletions, insertions and inversions) called with PAV and cross-validated with ten additional callers, with per-site carrier haplotype lists and structural annotations. </p> -<h3><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1 SVs</a></h3> +<h3><a href="hgTrackUi?g=cpc1Sv">CPC SVs</a></h3> <p> -Structural variants derived from the Human Pangenome Reference Consortium -release-2.1 minigraph-cactus pangenome graph, built from 233 PacBio HiFi -haplotype-resolved assemblies. ~541k SV-sized alleles (insertions and -deletions) extracted from the T2T-CHM13 graph with vg deconstruct. +Structural variants from the Chinese Pangenome Consortium (CPC), 58 samples +spanning 36 minority ethnic groups (PacBio HiFi pangenome graph; Gao et al. +2023). This track shows the CPC contribution to the joint CPC+HPRC graph with +HPRC-specific SVs removed. ~46k SVs (deletions, insertions and mixed snarls) in +native T2T-CHM13 coordinates. </p> <h3><a href="hgTrackUi?g=aprSv">Arab APR SVs</a></h3> <p> Structural variants from the Arab Pangenome Reference (APR), a haplotype-resolved pangenome graph built from 53 UAE-resident Arab individuals drawn from eight countries (PacBio HiFi + ultralong ONT + Hi-C; Nassir et al. 2025). ~103k SVs (deletions, insertions, complex and mixed snarls) in native T2T-CHM13 coordinates. </p> -<h3><a href="hgTrackUi?g=cpc1Sv">CPC SVs</a></h3> -<p> -Structural variants from the Chinese Pangenome Consortium (CPC), 58 samples -spanning 36 minority ethnic groups (PacBio HiFi pangenome graph; Gao et al. -2023). This track shows the CPC contribution to the joint CPC+HPRC graph with -HPRC-specific SVs removed. ~46k SVs (deletions, insertions and mixed snarls) in -native T2T-CHM13 coordinates. -</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 and other multi-allele events</span> - purple</li> </ul> </p> <h2>Data Access</h2> <p> Each subtrack has its own documentation page with details on how to download