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/decodeSv.html src/hg/makeDb/trackDb/human/decodeSv.html index 21dddbcebb1..4d3be32437c 100644 --- src/hg/makeDb/trackDb/human/decodeSv.html +++ src/hg/makeDb/trackDb/human/decodeSv.html @@ -1,113 +1,113 @@ <h2>Description</h2> <p> This track shows high-confidence structural variants (SVs) identified by Oxford Nanopore long-read sequencing of 3,622 Icelanders recruited through the deCODE genetics population cohort. The release contains 133,886 SVs (55,649 deletions, 75,050 insertions and 3,187 combined insertion/deletion events). Variants are site-level (no per-sample genotypes) and have been filtered to a high-confidence subset validated in the accompanying population-scale analysis. </p> <p> Note that this release does not include allele counts or allele frequencies: each row represents a site that was called with high confidence in the cohort, but the number of carrier samples is not provided, so the track cannot be filtered by AF/AC. </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(140,0,200);">Combined insertion/deletion (INSDEL)</span> - purple</li> </ul> </p> <p> Insertions are placed at the insertion site with a width of 1 bp; deletions span the deleted interval; INSDEL events span the affected reference region and have SVLEN=0 because the reference and alternate alleles differ in both sequence and length. Filters are available for SV type and SV length. </p> <p> Where a variant falls inside an annotated tandem-repeat region, the detail page also shows the coordinates of that region (TRRBEGIN / TRREND from the source VCF), which can be useful context for repeat-mediated insertions and deletions. </p> <h2>Methods</h2> <p> Beyter et al. 2021 performed Oxford Nanopore long-read sequencing of 3,622 Icelanders recruited through deCODE genetics and detected a median of 22,636 SVs per individual (13,353 insertions and 9,474 deletions). Across the cohort they derived a set of 133,886 reliably genotyped SV alleles, imputed those alleles into 166,281 chip-typed Icelanders, and tested them for association with disease and quantitative traits (notably including a rare <i>PCSK9</i> deletion associated with lower LDL-cholesterol and a multi-allelic 57-bp VNTR in <i>ACAN</i> associated with adult height). The track shown here displays 119,453 unique high-confidence SV sites (exact-duplicate records present in the release have been collapsed): 41,216 deletions, 75,050 insertions and 3,187 combined insertion/deletion events. The release is site-only (no per-sample genotypes or allele frequencies), so the track cannot be filtered by AF/AC. </p> <p> The VCF <tt>ont_sv_high_confidence_SVs.sorted.vcf.gz</tt> was downloaded from the deCODE genetics <a href="https://github.com/DecodeGenetics/LRS_SV_sets" target="_blank"> LRS_SV_sets</a> GitHub repository. </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 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 exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>decodeSv</i>. </p> <p> The annotation is stored as a bigBed file that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our download server</a> as <tt>decodeSv.bb</tt>. Individual regions or the whole annotation can be obtained with the <tt>bigBedToBed</tt> utility, available from our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">utilities page</a>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/decodeSv.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <p> The original VCF is available from the deCODE genetics <a href="https://github.com/DecodeGenetics/LRS_SV_sets" target="_blank">LRS_SV_sets</a> GitHub repository. </p> <h2>Credits</h2> <p> Thanks to the deCODE genetics team and the Icelandic study participants for making this dataset publicly available. </p> <h2>References</h2> <p> Beyter D, Ingimundardottir H, Oddsson A, Eggertsson HP, Bjornsson E, Jonsson H, Atlason BA, Kristmundsdottir S, Mehringer S, Hardarson MT <em>et al</em>. <a href="https://doi.org/10.1038/s41588-021-00865-4" target="_blank"> Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits</a>. <em>Nat Genet</em>. 2021 Jun;53(6):779-786. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33972781" target="_blank">33972781</a> </p>