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/aprSv.html src/hg/makeDb/trackDb/human/aprSv.html index 255e1ae719d..ac90c471788 100644 --- src/hg/makeDb/trackDb/human/aprSv.html +++ src/hg/makeDb/trackDb/human/aprSv.html @@ -1,103 +1,128 @@ <h2>Description</h2> <p> This track displays structural variants (SVs) — deletions, insertions, and complex substitutions of at least 50 bp — from the Arabic Pangenome Reference (APR), a pangenome graph built from 53 UAE-resident Arab individuals drawn from eight countries (UAE, Saudi Arabia, Oman, Jordan, Egypt, Morocco, Syria, Yemen). Each bubble in the graph that contains an SV-sized alternative allele is shown as a single variant site, with allele counts aggregated across the 53 samples (the GRCh38 reference haplotype, present as an extra sample column in the source VCF, is excluded from the aggregation).</p> <p> The APR pangenome was built on the T2T-CHM13v2 reference. Variants are shown natively on the <b>hs1</b> browser and lifted to <b>hg38</b> using the UCSC <tt>hs1ToHg38.over.chain.gz</tt> chain; variants that do not lift cleanly (often in T2T-added euchromatic sequence) are omitted from the hg38 version of the track.</p> <h2>Display conventions</h2> <p>Items are colored by SV type:</p> <ul> <li><span style="background-color:rgb(0,0,200);color:white;padding:1px 6px">INS</span> insertion (net ALT longer by ≥50 bp)</li> <li><span style="background-color:rgb(200,0,0);color:white;padding:1px 6px">DEL</span> deletion (net REF longer by ≥50 bp)</li> <li><span style="background-color:rgb(230,140,0);color:white;padding:1px 6px">CPX</span> complex substitution (similar-length REF and ALT but at least one ≥50 bp)</li> <li><span style="background-color:rgb(120,120,120);color:white;padding:1px 6px">MIXED</span> snarl whose alt alleles belong to different classes</li> </ul> <p>Each item spans from the start of REF to its end on the reference. The name field is the graph snarl ID (e.g. <tt><951452<1012008</tt>), which identifies the variant site in the APR pangenome graph.</p> <h2>Per-site alt-allele aggregation</h2> <p> The source VCF is multi-allelic: a single graph snarl appears as one row with a comma-separated ALT list. For this track, each ALT is classified individually using the 50 bp threshold, and the row is emitted as a single bed item with:</p> <ul> <li><b>svType</b> — the common class, or <tt>MIXED</tt> if alts disagree;</li> - <li><b>svLen</b> — the maximum |len(ALT)-len(REF)| across alts that passed;</li> - <li><b>alleleCount</b> — sum of per-alt allele counts (AC) that passed;</li> + <li><b>svLen</b> — reference span (chromEnd - chromStart);</li> + <li><b>insLen</b> — maximum inserted-sequence length across passing INS alts (0 otherwise);</li> + <li><b>AC</b> — sum of per-alt allele counts (AC) that passed;</li> <li><b>numAlts</b> — number of alt alleles that passed the 50 bp filter.</li> </ul> <p>Rows whose alts are all smaller than 50 bp are not shown.</p> <h2>Methods</h2> <p> -The APR pangenome was assembled from 53 individuals sequenced with an -average 35× PacBio HiFi, 54× ultralong ONT and 65× Hi-C -coverage, producing haplotype-phased de novo assemblies with N50 > 124 Mb. -The pangenome graph was built with Minigraph-Cactus v2.7.2 seeded on -CHM13v2 (backbone) and GRCh38; variants were extracted and deconstructed -from the graph. For this UCSC track, the decomposed VCF was parsed, -filtered to alt alleles with ≥50 bp REF/ALT length difference, and -merged per snarl site. See the build documentation in the kent source -tree at <tt>src/hg/makeDb/doc/hg38/lrSv.txt</tt> for details.</p> +Nassir et al. 2025 built the Arabic Pangenome Reference (APR) from 53 +UAE-resident Arab individuals drawn from eight countries, sequenced with +~35x PacBio HiFi on Sequel IIe/Revio (30-h movies), ~54x Oxford Nanopore +ultralong reads on R10.4.1 PromethION flow cells (96-h runs), and ~65x +Hi-C (Illumina NovaSeq 6000). Haplotype-phased de novo assemblies were +produced with hifiasm v0.19.5 (primary) and Verkko v1.3.1 (for +comparison), with a median N50 of 124 Mb. The pangenome graph was built +with Minigraph-Cactus seeded on T2T-CHM13v2 and augmented with GRCh38, +and SVs were extracted by graph deconstruction. The released decomposed +VCF (<tt>apr_review_v1_2902_chm13.vcf.gz</tt>) contains ~21 million +variants on CHM13v2 contigs; after filtering to alt alleles with ≥50 bp +length difference and collapsing the alts of each snarl into a single +site, the APR SV track is obtained. Variants are shown natively on hs1 +and lifted to hg38 with the UCSC <tt>hs1ToHg38.over.chain.gz</tt> chain +(variants not lifting cleanly are omitted from the hg38 version).</p> + +<p> +The source APR VCF was downloaded from the Mohammed Bin Rashid +University SharePoint page, +<a href="https://www.mbru.ac.ae/the-arab-pangenome-reference/" target="_blank"> +mbru.ac.ae/the-arab-pangenome-reference</a>; the accompanying project +source code is at +<a href="https://github.com/muddinmbru/arab_pangenome_reference" target="_blank"> +github.com/muddinmbru/arab_pangenome_reference</a>.</p> + +<p> +The step-by-step build commands (download, graph-VCF conversion, liftOver, +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 with the <a href="../cgi-bin/hgTables">Table Browser</a> or <a href="../cgi-bin/hgIntegrator">Data Integrator</a>, and accessed from scripts via our <a href="https://api.genome.ucsc.edu">API</a> (track=<i>aprSv</i>).</p> <p>For automated download, the bigBed files are at <a href="http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/apr.bb" target="_blank"> http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/apr.bb</a> (native) and <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/apr.bb" target="_blank"> http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/apr.bb</a> (lifted).</p> <p> The original APR pangenome VCF and assemblies can be downloaded from <a href="https://www.mbru.ac.ae/the-arab-pangenome-reference/" target="_blank"> https://www.mbru.ac.ae/the-arab-pangenome-reference/</a>, and the project source code is at <a href="https://github.com/muddinmbru/arab_pangenome_reference" target="_blank"> https://github.com/muddinmbru/arab_pangenome_reference</a>.</p> <h2>Credits</h2> <p>Thanks to the Arabic Pangenome Reference team at Mohammed Bin Rashid University (Dubai), led by Mohammed Uddin, for producing and releasing the pangenome and its variant calls.</p> <h2>References</h2> <p> Nassir N, Almarri MA, Kumail M, Mohamed N, Balan B, Hanif S, AlObathani M, Jamalalail B, Elsokary H, Kondaramage D <em>et al</em>. <a href="https://doi.org/10.1038/s41467-025-61645-w" target="_blank"> A draft UAE-based Arab pangenome reference</a>. <em>Nat Commun</em>. 2025 Jul 24;16(1):6747. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40707445" target="_blank">40707445</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12290100/" target="_blank">PMC12290100</a> </p>