6b0d68657267f1e02c47d4224ea62446bbbb2ba0 max Fri May 22 06:55:52 2026 -0700 small non-AI changes to the html docs pages of the long-read SV tracks diff --git src/hg/makeDb/trackDb/human/aprSv.html src/hg/makeDb/trackDb/human/aprSv.html index ac90c471788..107e2e2ef62 100644 --- src/hg/makeDb/trackDb/human/aprSv.html +++ src/hg/makeDb/trackDb/human/aprSv.html @@ -1,128 +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 +This track displays structural variants (SVs), at least 50 bp long +(deletions, insertions, and complex substitutions), 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> +<h2>Display Conventions and Configuration</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> +<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> — 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> + <li><b>svType</b>: the common class, or <tt>MIXED</tt> if alts disagree;</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> 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>