9fbdfa3416ffde377072fafd2de44059155c3b44 max Thu Apr 30 06:57:35 2026 -0700 lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642 diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index 65ed0a19bcc..ae8d30a51e9 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -12,306 +12,340 @@ SV length statistics (min / median / max) are computed from the <tt>svLen</tt> field of each track, in base pairs. Some tracks include sites with <tt>svLen=0</tt> (complex events where the reference and alternate alleles differ in sequence but not in length). </p> <p> For short-read structural-variant comparators (CCDG 17,795, 1KG 3202, ToMMo 48K CNV) see the companion <a href="hgTrackUi?g=srSv">Short-read SVs</a> supertrack. </p> <table class="stdTbl"> <tr> <th>Dataset</th> <th>N samples</th> <th>Cohort / disease</th> + <th>Disease cases</th> <th>Sequencing</th> <th>SVs</th> <th>Min</th> <th>Median</th> <th>Max</th> </tr> +<tr> + <td><a href="hgTrackUi?g=lrSvAll"><b>All merged</b></a></td> + <td>—</td> + <td>All long-read SV datasets merged on identical position+type+length, with per-database AC</td> + <td>mixed</td> + <td>mixed (PacBio HiFi, ONT)</td> + <td>2,694,871</td> + <td>50</td> + <td>200</td> + <td>190,088,223</td> +</tr> <tr> <td><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb</a></td> <td>1,427</td> <td>Consortium of Long-Read Sequencing, joint callset</td> + <td>No</td> <td>PacBio HiFi</td> <td>426,239</td> <td>20</td> <td>33</td> <td>101,381</td> </tr> <tr> <td><a href="hgTrackUi?g=han945Sv">Han 945</a></td> <td>945</td> <td>Han Chinese, general population</td> + <td>No</td> <td>ONT (PromethION)</td> <td>111,288</td> <td>0</td> <td>254</td> <td>99,743</td> </tr> <tr> <td><a href="hgTrackUi?g=gustafsonSv">1KG ONT 100</a></td> <td>100</td> - <td>1000 Genomes, 5 superpopulations / 19 subpopulations</td> + <td>1000 Genomes, 5 superpopulations / 19 subpop., high 37x seq. coverage</td> + <td>No</td> <td>ONT (R9.4.1)</td> <td>113,696</td> <td>0</td> <td>164</td> <td>98,289</td> </tr> <tr> <td><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a></td> <td>1,019</td> - <td>1000 Genomes, globally diverse</td> + <td>1000 Genomes, diverse, normal 17x seq. coverage</td> + <td>No</td> <td>ONT</td> <td>148,375</td> <td>2</td> <td>177</td> <td>49,171</td> </tr> <tr> <td><a href="hgTrackUi?g=tommoJpSv">ToMMo Japanese</a></td> <td>333 (111 trios)</td> <td>Japanese, general population</td> + <td>No</td> <td>ONT</td> <td>74,201</td> <td>51</td> <td>162</td> <td>99,980</td> </tr> <tr> <td><a href="hgTrackUi?g=aou1kSv">AoU 1K</a></td> <td>1,027</td> - <td>All of Us, self-identified Black/African American</td> + <td>All of Us, self-identified Black/African American, 8x cov.; biobank includes a variety of conditions (diabetes, hearing loss, etc.)</td> + <td>Yes (mixed)</td> <td>PacBio HiFi</td> <td>541,049</td> <td>50</td> <td>152</td> <td>9,998</td> </tr> <tr> <td><a href="hgTrackUi?g=ga4kSv">GA4K</a></td> <td>502</td> <td>Children's Mercy, pediatric rare disease probands + families</td> + <td>Yes (probands)</td> <td>PacBio HiFi</td> <td>115,554</td> <td>50</td> <td>186</td> <td>809,711</td> </tr> <tr> <td><a href="hgTrackUi?g=decodeSv">deCODE 3,622</a></td> <td>3,622</td> <td>Icelandic general population</td> + <td>No</td> <td>ONT</td> <td>133,886</td> <td>0</td> <td>127</td> <td>861,080</td> </tr> <tr> <td><a href="hgTrackUi?g=hprc2Sv">HPRC v2</a></td> <td>233</td> <td>HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies)</td> + <td>No</td> <td>PacBio HiFi (pangenome graph)</td> <td>1,483,114</td> <td>50</td> <td>280</td> <td>97,718</td> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2</a></td> <td>32</td> <td>HGSVC2 haplotype-resolved assemblies (5 superpopulations)</td> + <td>No</td> <td>PacBio CLR + HiFi + Strand-seq</td> <td>111,746</td> <td>50</td> <td>168</td> <td>57,207,414</td> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td> <td>65</td> <td>HGSVC3 diverse reference assemblies</td> + <td>No</td> <td>PacBio HiFi + ONT</td> <td>176,531</td> <td>50</td> <td>154</td> <td>30,176,500</td> </tr> <tr> - <td><a href="hgTrackUi?g=aprSv">Arab APR</a></td> + <td><a href="hgTrackUi?g=aprSv">Arab UPR</a></td> <td>53</td> - <td>UAE-resident Arabs from 8 countries (Arab Pangenome Reference)</td> + <td>UAE-resident Arabs from 8 countries (UAE Pangenome Reference)</td> + <td>No</td> <td>PacBio HiFi + ONT + Hi-C (pangenome graph)</td> <td>72,656</td> <td>1</td> <td>21</td> <td>99,885</td> </tr> <tr> <td><a href="hgTrackUi?g=cpc1Sv">CPC</a></td> <td>58</td> <td>Chinese Pangenome Consortium, 36 minority ethnic groups (HPRC-specific SVs removed)</td> + <td>No</td> <td>PacBio HiFi (pangenome graph)</td> <td>36,030</td> <td>1</td> <td>53</td> <td>8,998,096</td> </tr> <tr> <td><a href="hgTrackUi?g=kwanhoSv">Kim PD Brain</a></td> <td>100</td> <td>Parkinson's disease, ILBD, controls (post-mortem brain)</td> + <td>Yes (PD + ILBD)</td> <td>PacBio HiFi</td> <td>74,552</td> <td>50</td> <td>160</td> <td>190,088,222</td> </tr> <tr> <td><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101</a></td> <td>101</td> - <td>Long-read WGS cohort for GWAS LD fine-mapping (SickKids)</td> + <td>Cystic fibrosis (CF) patients from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT). Long-read WGS used for GWAS LD fine-mapping</td> + <td>Yes (all CF)</td> <td>long-read</td> <td>87,183</td> <td>4</td> <td>160</td> <td>1,321,484</td> </tr> </table> <p> Note: there is likely some overlap in sample composition across these collections. For example, 1000 Genomes samples are also included in HPRC and CoLoRSdb. </p> -<h3>CoLoRSdb SVs (<a href="hgTrackUi?g=colorsDbSv">colorsDbSv</a>)</h3> +<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. -426,239 SVs (insertions, deletions, inversions) called with pbsv and +~426k 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>Han 945 SVs (<a href="hgTrackUi?g=han945Sv">han945Sv</a>)</h3> +<h3><a href="hgTrackUi?g=han945Sv">Han 945 SVs</a></h3> <p> -Structural variants from 945 Han Chinese individuals. 111,288 SVs +Structural variants from 945 Han Chinese individuals. ~111k SVs (deletions, insertions, duplications, inversions, translocations) merged with SURVIVOR. Includes allele frequencies and per-sample support. </p> -<h3>1KG ONT 100 SVs (<a href="hgTrackUi?g=gustafsonSv">gustafsonSv</a>)</h3> +<h3><a href="hgTrackUi?g=gustafsonSv">1KG ONT 100 SVs</a></h3> <p> Structural variants from Oxford Nanopore long-read sequencing of 100 1000 Genomes samples (5 superpopulations, 19 subpopulations) released by the 1000 Genomes ONT Sequencing Consortium and described in -Gustafson et al. 2024. 113,696 SVs (insertions, deletions, duplications, +Gustafson et al. 2024. ~114k SVs (insertions, deletions, duplications, inversions) called with five callers and merged with Jasmine. This is a separate dataset from the Vienna 1KG-ONT release below; the 100 samples here do not overlap with the 1,019 samples in the Vienna release. </p> -<h3>1KG ONT Vienna SVs (<a href="hgTrackUi?g=lrSv1kgOnt">lrSv1kgOnt</a>)</h3> +<h3><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna SVs</a></h3> <p> Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT). -161,332 SVs annotated with SVAN, classifying insertions and deletions by mechanism +~161k SVs annotated with SVAN, classifying insertions and deletions by mechanism of origin (mobile elements, VNTRs, processed pseudogenes, etc.). Original coordinates are on T2T-CHM13 (hs1); the hg38 version was created via liftOver. This is a separate dataset from the 1KG ONT 100 (Gustafson et al.) track above; the 1,019 samples here do not overlap with the 100 samples in that release. </p> -<h3>ToMMo Japanese SVs (<a href="hgTrackUi?g=tommoJpSv">tommoJpSv</a>)</h3> +<h3><a href="hgTrackUi?g=tommoJpSv">ToMMo Japanese SVs</a></h3> <p> Structural variants from 333 Japanese individuals (111 trios) from the Tohoku Medical -Megabank (ToMMo). 74,201 SVs (deletions and insertions) with trio-based Mendelian +Megabank (ToMMo). ~74k SVs (deletions and insertions) with trio-based Mendelian error rates and allele frequencies. </p> -<h3>AoU 1K SVs (<a href="hgTrackUi?g=aou1kSv">aou1kSv</a>)</h3> +<h3><a href="hgTrackUi?g=aou1kSv">AoU 1K SVs</a></h3> <p> Structural variants from 1,027 individuals from the All of Us (AoU) Research Program, -sequenced with PacBio HiFi long reads. 541,049 SVs (insertions and deletions) -with population-specific allele frequencies, gene annotations, and clinical -trait associations. +sequenced with PacBio HiFi long reads. AoU is a deeply phenotyped biobank +that includes participants with a range of conditions (e.g. diabetes, +hearing loss, hypertension), so the cohort is not disease-free. +~541k SVs (insertions and deletions) with population-specific allele +frequencies, gene annotations, and clinical trait associations. </p> -<h3>GA4K SVs (<a href="hgTrackUi?g=ga4kSv">ga4kSv</a>)</h3> +<h3><a href="hgTrackUi?g=ga4kSv">GA4K SVs</a></h3> <p> Structural variants from 502 probands and family members enrolled in the Genomic Answers for Kids (GA4K) pediatric rare-disease program at Children's -Mercy Research Institute, sequenced with PacBio HiFi long reads. 115,554 +Mercy Research Institute, sequenced with PacBio HiFi long reads. ~116k replicated SVs (deletions, insertions, duplications, inversions) called with pbsv and merged with JASMINE. The matched GA4K small-variant callset (SNVs and short indels) lives alongside other population allele-frequency resources as <a href="hgTrackUi?g=ga4kSnv">GA4K 552 PacBio LR</a> in the Variant Frequencies track collection. </p> -<h3>deCODE 3,622 SVs (<a href="hgTrackUi?g=decodeSv">decodeSv</a>)</h3> +<h3><a href="hgTrackUi?g=decodeSv">deCODE 3,622 SVs</a></h3> <p> High-confidence structural variants from 3,622 Icelanders (deCODE genetics), -sequenced with Oxford Nanopore long reads. 133,886 SVs (deletions, insertions +sequenced with Oxford Nanopore long reads. ~134k SVs (deletions, insertions and combined insertion/deletion events). Site-only callset with annotated surrounding tandem-repeat regions. </p> -<h3>HPRC v2 SVs (<a href="hgTrackUi?g=hprc2Sv">hprc2Sv</a>)</h3> +<h3><a href="hgTrackUi?g=hprc2Sv">HPRC v2 SVs</a></h3> <p> Structural variants derived from the Human Pangenome Reference Consortium release-2 minigraph-cactus pangenome graph, built from 233 PacBio HiFi haplotype-resolved assemblies (CHM13 + diverse 1000 Genomes samples). -1,483,114 SV-sized alleles (INS, DEL, COMPLEX, INV) extracted with +~1.5M SV-sized alleles (INS, DEL, COMPLEX, INV) extracted with <tt>vg deconstruct</tt> and decomposed with <tt>vcfwave</tt> (WFA2). </p> -<h3>HGSVC2 32 SVs (<a href="hgTrackUi?g=hgsvc2Sv">hgsvc2Sv</a>)</h3> +<h3><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2 32 SVs</a></h3> <p> Structural variants from 32 haplotype-resolved diploid genomes (HGSVC2 -freeze 4, Ebert et al. 2021). 111,746 SVs (deletions, insertions and +freeze 4, Ebert et al. 2021). ~112k SVs (deletions, insertions and inversions) called from phased de novo assemblies with PAV, with per-variant 1000 Genomes population allele frequencies (insertions and deletions) and rich structural/gene annotations. An earlier HGSVC release complementary to <a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a>. </p> -<h3>HGSVC3 65 SVs (<a href="hgTrackUi?g=hgsvc3Sv">hgsvc3Sv</a>)</h3> +<h3><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3 65 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). 176,532 haplotype-resolved SVs (deletions, insertions and +(HGSVC3). ~177k 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>Kim PD Brain SVs (<a href="hgTrackUi?g=kwanhoSv">kwanhoSv</a>)</h3> +<h3><a href="hgTrackUi?g=kwanhoSv">Kim PD Brain SVs</a></h3> <p> Structural variants from 100 post-mortem brain samples (Parkinson's disease, incidental Lewy body disease, and healthy controls) sequenced with PacBio -HiFi long reads. 74,552 high-confidence SVs (deletions, insertions, +HiFi long reads. ~75k high-confidence SVs (deletions, insertions, duplications, inversions) with per-cohort allele frequencies and case-control carrier-rate differentials, from Kim et al. 2026. </p> -<h3>SVatalog 101 SVs (<a href="hgTrackUi?g=chirmade101Sv">chirmade101Sv</a>)</h3> +<h3><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101 SVs</a></h3> <p> Structural variants from 101 long-read whole-genome sequences released -alongside the GWAS SVatalog tool (Chirmade et al. 2026). 87,183 SVs +alongside the GWAS SVatalog tool (Chirmade et al. 2026). The samples come +from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT), a +cystic-fibrosis (CF) patient cohort assembled to model patient-specific +responses to CFTR modulator therapies (most participants are F508del +homozygotes or F508del / minimal-function compound heterozygotes; a smaller +number carry rare nonsense or missense CFTR mutations). ~87k SVs (deletions, insertions, duplications, inversions and complex events) annotated with gene overlaps, ClinGen / gnomAD constraint scores, OMIM / ClinVar / DGV / Decipher regional annotations. </p> <h2>Data Access</h2> <p> Each subtrack has its own documentation page with details on how to download and intersect the underlying annotations. </p> <h2>References</h2> <p>