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/lrSv1kgOnt.html src/hg/makeDb/trackDb/human/lrSv1kgOnt.html index b678593dd8c..9a379e674a6 100644 --- src/hg/makeDb/trackDb/human/lrSv1kgOnt.html +++ src/hg/makeDb/trackDb/human/lrSv1kgOnt.html @@ -1,97 +1,117 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) identified by Oxford Nanopore long-read sequencing of 1,019 individuals from the 1000 Genomes Project, representing 26 populations across 5 continental regions: Africa (275 samples), East Asia (192), South Asia (199), Europe (189), and Americas (164). Median sequencing coverage was 16.9x per sample with a median N50 read length of 20.3 kb. </p> <p> SVs were discovered using the SAGA framework (SV Analysis by Graph Augmentation) and annotated with SVAN, which classifies insertions and deletions by their mechanism of origin. The dataset contains 161,332 annotated SVs, including 75,324 insertions, 66,192 deletions, and 19,816 complex rearrangements. The original coordinates are on the T2T-CHM13 assembly (hs1); for GRCh38 (hg38), coordinates were converted using liftOver (148,375 records mapped successfully). </p> +<p> +The 1,019 samples sequenced here are distinct from those in the +<a href="hgTrackUi?g=gustafsonSv">1KG ONT 100</a> track (Gustafson et al. 2024); +the two releases were produced by separate consortia (Vienna and the 1000 Genomes +ONT Sequencing Consortium, respectively) and there is no sample overlap between +the two. +</p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV class: <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(230,140,0);">Complex (COMPLEX)</span> - orange</li> +<li><span style="color: rgb(230,140,0);">Complex (CPX)</span> - orange</li> </ul> </p> <p> -Filters are available for SV class, insertion/deletion type, transposon family, +Filters are available for SV type, insertion/deletion type, transposon family, and SV length. For insertions, the item is placed at the insertion site with a width of 1 bp; for deletions, the item spans the deleted region. </p> <p> The detail page for each item shows SVAN annotation fields including: <ul> <li><b>Insertion/Deletion Type</b>: solo (single mobile element), partnered (with transduction), orphan (transduction only), VNTR, PSD (processed pseudogene), NUMT (nuclear mitochondrial insertion), DUP (tandem duplication), DUP_INTERSPERSED, INV_DUP (inverted duplication), COMPLEX_DUP, or chimera</li> <li><b>Transposon Family</b>: Alu, L1, SVA, HERVK, or LTR5_Hs</li> <li><b>Percent Resolved</b>: fraction of inserted sequence resolved by assembly</li> <li><b>TSD Length</b>: target site duplication length</li> <li><b>Poly-A Length</b>: poly-A tail length</li> <li><b>Conformation</b>: structural conformation of the insertion (e.g. FOR+POLYA, Hexamer+Alu-like+VNTR+SINE-R+POLYA)</li> <li><b>Source Coordinates</b>: genomic location of the source element (for transductions)</li> </ul> </p> <h2>Methods</h2> <p> -Oxford Nanopore sequencing was performed on 1,019 samples from the 1000 Genomes -Project. Base-calling was done with Guppy 6.2.1. SVs were discovered using -the SAGA framework, which combines: -<ul> -<li>Linear-reference tools: Sniffles and DELLY (applied to both GRCh38 and CHM13)</li> -<li>Graph-aware discovery: SVarp, which searches for SV patterns from graph-aligned -reads and performs local long-read assembly</li> -<li>Graph-based genotyping: Giggles, for unified genotyping across a pangenome graph</li> -</ul> +Schloissnig et al. 2025 generated intermediate-coverage Oxford Nanopore +long-read sequencing of 1,019 samples from the 1000 Genomes Project on +PromethION 48 instruments with R9.4.1 (FLO-PRO002) flow cells (SQK-LSK110 +libraries, 24-h runs with flow-cell wash and reload). SVs were discovered +with the SAGA framework (SV Analysis by Graph Augmentation), which combines +linear-reference callers (Sniffles and DELLY, run against both GRCh38 and +T2T-CHM13), graph-aware discovery with SVarp (local long-read assembly of +SV-supporting graph-aligned reads) and graph-based joint genotyping with +Giggles across a pangenome graph. Insertions and deletions were then +annotated with <a href="https://github.com/REPBIO-LAB/svan" target="_blank"> +SVAN</a> v1.3, which classifies SVs by mechanism of origin. The release +contains 161,332 SVAN-annotated SVs: 75,324 insertions, 66,192 deletions +and 19,816 complex rearrangements. The original VCF is on T2T-CHM13 contig +coordinates; for the hg38 version of this track, SVs were lifted with +liftOver (148,375 of 161,332 records mapped), while the hs1 version uses +the native coordinates. </p> <p> -Variants were annotated with SVAN (SV Annotator v1.3), which leverages allelic -representations and genomic annotations to classify SVs by mechanism. SVAN -annotated 96.0% of insertions, 32.2% of deletions, and 57.1% of complex sites. +The SVAN-annotated unphased VCF (<tt>final-vcf.unphased.SVAN_1.3.vcf.gz</tt>) +was downloaded from +<a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/release/v1.1/svan-annotation/" target="_blank"> +the IGSR 1KG_ONT_VIENNA v1.1 SVAN-annotation directory</a>; allele counts +were added from the companion shapeit5-phased-callset +(<tt>shapeit5-phased-callset_final-vcf.phased.vcf.gz</tt>) in the same +release tree. </p> <p> -The original SV coordinates are on the T2T-CHM13 assembly (hs1). For the GRCh38 -(hg38) version of this track, coordinates were converted using liftOver; 148,375 -of 161,332 records mapped successfully (~92%). The hs1 version contains all -161,332 records at their native coordinates. +The step-by-step build commands (download, liftOver, 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> Source data is available from the <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/" target="_blank">1000 Genomes ONT Vienna</a> data collection at IGSR. </p> <h2>Credits</h2> <p> Thanks to the 1000 Genomes ONT Vienna consortium for making their structural variant calls and SVAN annotations publicly available. </p> <h2>References</h2> <p> Schloissnig S, Pani S, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M <em>et al</em>. <a href="https://doi.org/10.1038/s41586-025-09290-7" target="_blank"> Structural variation in 1,019 diverse humans based on long-read sequencing</a>. <em>Nature</em>. 2025 Aug;644(8076):442-452. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702182" target="_blank">40702182</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350158/" target="_blank">PMC12350158</a> </p>