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/hgsvc2Sv.html src/hg/makeDb/trackDb/human/hgsvc2Sv.html index 500ba0a04f9..994ff8c8441 100644 --- src/hg/makeDb/trackDb/human/hgsvc2Sv.html +++ src/hg/makeDb/trackDb/human/hgsvc2Sv.html @@ -1,122 +1,135 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) from the second phase of the Human Genome Structural Variation Consortium (HGSVC2). The callset is derived from 32 haplotype-resolved diploid genomes (64 phased haplotypes) spanning five 1000 Genomes superpopulations (African, Admixed American, East Asian, European, South Asian). Each genome was sequenced with PacBio long reads (continuous long-read and HiFi) and phased with Strand-seq, enabling comprehensive characterization of SVs that short-read approaches miss. </p> <p> The track merges the two SV annotation tables from the HGSVC2 v2.0 integrated callset freeze 4: 111,330 insertions/deletions and 416 inversions, for a total of 111,746 SVs. Each row is a site-level variant with per-site allele count, carrier haplotypes, population-scale allele frequencies (imputed from the phased callset back into 1000 Genomes, insertions and deletions only) and structural annotations. </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(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 and inversions span the affected reference interval. Filters are available for SV type, SV length, carrier-haplotype count, distinct sample count, whether the site falls in a Tandem Repeat Finder region and the fraction of the variant overlapping segmental duplications. </p> <p> The detail page shows, where available: <ul> <li><b>Allele / Sample Count</b>: carrier-haplotype count (MERGE_AC) and the number of distinct samples carrying the variant.</li> <li><b>Population Allele Frequencies</b> (insertions and deletions only): overall and per-population (AFR, AMR, EAS, EUR, SAS) allele frequencies computed from the imputed 1000 Genomes callset.</li> <li><b>RefSeq Gene Overlaps</b>: bases of overlap with CDS, 5'/3' UTRs, introns, non-coding RNAs, and +/- 5 kb windows around each gene.</li> <li><b>Gene Constraint</b>: maximum gnomAD pLI and minimum LOEUF upper bound for genes overlapping the SV.</li> <li><b>Reference Context</b>: cytoband, segmental-duplication overlap, whether the SV falls in a Tandem Repeat Finder region.</li> <li><b>Carrier Haplotypes</b>: full list of sample-haplotype IDs (e.g. <tt>HG00096-h1</tt>, <tt>HG00514-un</tt>) carrying the variant.</li> <li><b>Inner Inversion Region</b> (INV only): coordinates of the inner inverted sequence, distinct from the outer breakpoint interval.</li> </ul> </p> <h2>Methods</h2> <p> -HGSVC2 generated phased haplotype-resolved de novo assemblies for 32 -diploid samples across five 1000 Genomes superpopulations. Assemblies -were built from PacBio continuous long reads and HiFi reads and phased -with Strand-seq. Structural variants were discovered from each haplotype -assembly using PAV and validated with multiple orthogonal callers -(including PBSV, Bionano, DeepVariant, PAV-LRA, and others recorded in -per-site validation columns). The final SV set was merged to produce the -integrated callset used here. +Ebert et al. 2021 produced phased haplotype-resolved de novo assemblies for +32 diploid samples (64 unrelated haplotypes) across five 1000 Genomes +superpopulations on the PacBio Sequel II platform, using continuous +long-read sequencing (CLR, >40x) and high-fidelity sequencing (HiFi, +>20x). Single-cell Strand-seq data from the same samples were used to +phase the assemblies without parental trios, yielding N50 contigs >25 Mbp +at QV > 40. SVs were discovered from the two haplotype assemblies of +each sample with the Phased Assembly Variant (PAV) caller against GRCh38, +and candidate SVs were orthogonally supported by at least one of seven +other sources (read-based callers MELT, PBSV and PALMER; Bionano optical +mapping; breakpoint k-mer analysis; PAV replication with LRA). This +yielded the integrated nonredundant callset of 107,590 insertion/deletion +SVs and 316 inversions. Population-scale allele frequencies (POP_*_AF) were +obtained by graph-based re-genotyping of the HGSVC2 SVs into the +3,202-sample 1000 Genomes short-read cohort with PanGenie (insertions and +deletions only). </p> <p> -Population-scale allele frequencies (POP_*_AF) were derived by imputing -the HGSVC2 SVs back into the full 1000 Genomes short-read cohort. These -fields are only available for insertions and deletions. +For display, the HGSVC2 v2.0 freeze-4 annotation tables +<tt>variants_freeze4_sv_insdel.tsv.gz</tt> (111,330 DEL+INS) and +<tt>variants_freeze4_sv_inv.tsv.gz</tt> (416 INV) were downloaded from the +<a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/release/v2.0/integrated_callset/" target="_blank"> +IGSR HGSVC2 v2.0 integrated-callset directory</a> and merged into a single +bigBed; type-specific columns (POP_*_AF for insdel, RGN_REF_INNER for +inversions) are empty on the detail page when they do not apply. </p> <p> -Two tables were merged for display here: -<tt>variants_freeze4_sv_insdel.tsv.gz</tt> (DEL + INS, 111,330 records) and -<tt>variants_freeze4_sv_inv.tsv.gz</tt> (INV, 416 records). Type-specific -columns (POP_*_AF for insdel, RGN_REF_INNER for inversions) are shown as -empty on the detail page when they do not apply. +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>hgsvc2Sv</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>hgsvc2.bb</tt>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/hgsvc2.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <p> The original annotation tables and VCFs are available from the <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/release/v2.0/integrated_callset/" target="_blank"> HGSVC2 v2.0 integrated callset</a> on the IGSR FTP site. </p> <h2>Credits</h2> <p> Thanks to the Human Genome Structural Variation Consortium (HGSVC) and the 1000 Genomes Project for releasing this dataset. Later HGSVC releases are also available as UCSC tracks: <a href="hgTrackUi?g=hgsvc3Sv">HGSVC3 65 SVs</a>. </p> <h2>References</h2> <p> Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R <em>et al</em>. <a href="https:///www.science.org/doi/10.1126/science.abf7117" target="_blank"> Haplotype-resolved diverse human genomes and integrated analysis of structural variation</a>. <em>Science</em>. 2021 Apr 2;372(6537). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33632895" target="_blank">33632895</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026704/" target="_blank">PMC8026704</a> </p>