bac95a147f49cd331052e597006e04b3deee40fc max Wed Apr 22 10:43:20 2026 -0700 lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258 diff --git src/hg/makeDb/trackDb/human/decodeSv.html src/hg/makeDb/trackDb/human/decodeSv.html index c5ba7bf869d..e5940527f8c 100644 --- src/hg/makeDb/trackDb/human/decodeSv.html +++ src/hg/makeDb/trackDb/human/decodeSv.html @@ -27,38 +27,56 @@ <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> -Oxford Nanopore whole-genome sequencing was performed on 3,622 Icelandic -participants enrolled through deCODE genetics. Reads were aligned to -GRCh38 and structural variants were called and merged across the cohort -following the pipeline described in Beyter et al. (2021), which combined -multiple callers and a joint reassessment of candidate variants against -the long reads. The high-confidence set released here corresponds to the -filtered callset with strong read support and consistent representation -across samples. +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 the 133,886 high-confidence SV sites: 55,649 +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>. </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