2e0addd016cfcbf61485b90d8980a8d75be622c2 lrnassar Sun Jun 14 00:10:06 2026 -0700 lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released). diff --git src/hg/makeDb/trackDb/human/gustafsonSv.html src/hg/makeDb/trackDb/human/gustafsonSv.html index e31e5a7bc66..c2d21fdad24 100644 --- src/hg/makeDb/trackDb/human/gustafsonSv.html +++ src/hg/makeDb/trackDb/human/gustafsonSv.html @@ -1,116 +1,117 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) from Oxford Nanopore long-read whole-genome sequencing of 100 individuals in the 1000 Genomes Project, as released by the 1000 Genomes Project ONT Sequencing Consortium and described in Gustafson et al. 2024. The cohort spans all five 1000 Genomes superpopulations and 19 subpopulations. Samples were sequenced with ONT R9.4.1 pores at ~37x coverage with median read N50 of ~54 kb. </p> <p> -The track contains 113,696 SVs (63,177 insertions, 49,704 deletions, -744 inversions, 71 duplications). Each variant was called by up to five +The track contains 113,159 SVs (63,177 insertions, 49,700 deletions, +211 inversions, 71 duplications; byte-identical duplicate records have been +removed). Each variant was called by up to five independent methods (three alignment-based: Sniffles2, cuteSV, SVIM; and assembly-based hapdiff on Flye or Shasta/Hapdup assemblies) and then merged across callers and samples with Jasmine to produce a cross-sample consensus catalog. </p> <p> This 100-sample Gustafson cohort is distinct from the Vienna 1000-Genomes-ONT release (<a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT SVs</a>), which uses different samples, pore chemistry and callers; the two releases share neither samples nor calls. </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> </ul> </p> <p> Insertions are placed at the insertion site with a width of 1 bp; deletions, duplications and inversions span the affected reference interval. Filters are available for SV type, SV length and carrier-sample count. The detail page also shows the number of per-caller calls supporting each site (VARCALLS) and whether the source caller marked the breakpoints as precise. </p> <h2>Methods</h2> <p> Gustafson et al. 2024 performed Oxford Nanopore long-read sequencing on 100 samples from the 1000 Genomes Project (all five superpopulations and 19 subpopulations) using R9.4.1 flow cells, at a median per-sample coverage of ~37x and read N50 of ~54 kb. Per-sample SV calls were generated through the Napu pipeline with five independent methods: three alignment-based callers (Sniffles2, cuteSV and SVIM run on minimap2 alignments to GRCh38) and two assembly-based callers (hapdiff run on Flye and on Shasta/Hapdup assemblies). The five per-sample VCFs were merged with <a href="https://github.com/mkirsche/Jasmine" target="_blank">Jasmine</a> in two stages (intra-sample consensus, then cross-sample merge). The released confident site-level callset is defined as variants supported by hapdiff and at least two unique alignment-based callers, yielding 113,696 SVs (63,177 insertions, 49,704 deletions, 744 inversions, 71 duplications). SV counts per sample and multicaller concordance were benchmarked against the HPRC Sniffles2 truth and the GIAB HG002 Tier1 region with Truvari v4.1.0. </p> <p> The source Jasmine-merged VCF was downloaded from the 1000 Genomes ONT S3 bucket: <a href="https://s3.amazonaws.com/1000g-ont/Gustafson_etal_2024_preprint_SUPPLEMENTAL/20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz" target="_blank"> <tt>20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz</tt></a>. </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>. </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>gustafsonSv</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>gustafson.bb</tt>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/gustafson.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <p> The original VCF is available from the 1000 Genomes ONT S3 bucket: <a href="https://s3.amazonaws.com/1000g-ont/Gustafson_etal_2024_preprint_SUPPLEMENTAL/20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz" target="_blank"> 20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz</a>. </p> <h2>Credits</h2> <p> Thanks to Gustafson and colleagues and the 1000 Genomes Project ONT Sequencing Consortium for releasing this dataset. </p> <h2>References</h2> <p> Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W <em>et al</em>. <a href="http://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=39358015" target="_blank"> High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation</a>. <em>Genome Res</em>. 2024 Nov 20;34(11):2061-2073. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39358015" target="_blank">39358015</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610458/" target="_blank">PMC11610458</a> </p>