526213b2893134217a300ff913e11b4e98d67991 max Mon Apr 20 08:50:10 2026 -0700 lrSv: add cpc1Sv and aprSv pangenome SV subtracks (hg38, hs1) cpc1Sv: 97,205 SVs from the CPC + HPRC Phase 1 pangenome (Gao et al 2023, Nature; PMID 37316654) built on T2T-CHM13v2, with 53 Chinese and 47 HPRC samples. Each graph snarl site is shown as one item with alt alleles classified by length delta (INS/DEL/CPX, 50 bp threshold) and collapsed. aprSv: 103,077 SVs from the Arabic Pangenome Reference (Nassir et al. 2025, Nat Commun; PMID 40707445) built on T2T-CHM13v2 from 53 UAE-resident Arab individuals. Same multi-allele classification as cpc1Sv, with alt alleles iterated within each multi-allelic row. Both tracks load natively on hs1 and are lifted to hg38 with hs1ToHg38.over.chain.gz. refs #36258 diff --git src/hg/makeDb/trackDb/human/cpc1Sv.html src/hg/makeDb/trackDb/human/cpc1Sv.html new file mode 100644 index 00000000000..e3f5e3f01a7 --- /dev/null +++ src/hg/makeDb/trackDb/human/cpc1Sv.html @@ -0,0 +1,120 @@ +<h2>Description</h2> + +<p> +This track displays structural variants (SVs) — deletions, insertions, and +complex substitutions of at least 50 bp — identified by the Chinese +Pangenome Consortium (CPC) from a pangenome graph built from 58 core samples +representing 36 Chinese minority ethnic groups, jointly with 47 samples from +Phase 1 of the Human Pangenome Reference Consortium (HPRC). After +decomposition of the graph bubbles, each distinct graph site (snarl) is +displayed as one variant record, with genotypes aggregated across 105 +samples.</p> + +<p> +A pangenome is a graph that represents many genomes simultaneously, letting +variants that are missing from a single linear reference be captured and +typed directly. Because the CPC pangenome was built on the T2T-CHM13v2 +assembly, variants are shown natively on the hs1 browser and lifted to hg38 +using the UCSC <tt>hs1ToHg38.over.chain.gz</tt> chain. About 16% of the +97,205 hs1 sites did not lift over cleanly (usually in highly repetitive +regions added to T2T-CHM13).</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 collapsed alt alleles belong to different classes</li> +</ul> + +<p> +Each bed item spans from the start of the REF allele to its end on the +reference. Pure insertions (where REF is a single base) therefore appear +as narrow single-base marks; DELs and CPX items span the affected reference +interval.</p> + +<p> +The <i>name</i> field is the graph snarl ID (two node identifiers separated +by strand arrows, e.g. <tt>>2541>2547</tt>). It is stable across the +graph but has no meaning outside the CPC pangenome graph file.</p> + +<h2>Collapsing of multi-allelic sites</h2> + +<p> +The source VCF was decomposed with <tt>bcftools norm -m -any</tt>, so each +graph snarl appears as one VCF row per alternative allele (a single +bubble in the graph may have 2-20+ alt paths). For display, all alternative +alleles sharing the same snarl ID are collapsed into one track item:</p> +<ul> + <li><b>SV type</b> is the common class of all alts, or <tt>MIXED</tt> if + they disagree (for example one alt is a DEL and another is an INS).</li> + <li><b>SV length</b> is the maximum |len(ALT) − len(REF)| across alts.</li> + <li><b>Allele count</b> is the sum of the per-alt allele counts.</li> + <li><b>Number of alts</b> records how many alternative alleles were merged.</li> +</ul> + +<h2>Filters</h2> + +<p>Available filters:</p> +<ul> + <li><b>SV type</b> — any combination of INS, DEL, CPX, MIXED.</li> + <li><b>SV length</b> — maximum allele-length difference.</li> + <li><b>Allele frequency</b> and <b>allele count</b> across the combined + 105 samples.</li> +</ul> + +<h2>Methods</h2> + +<p> +The CPC assemblies were produced from PacBio HiFi long-read sequencing +(mean ~30× coverage) with <a href="https://github.com/chhylp123/hifiasm" target="_blank">hifiasm</a> +in trio or Hi-C-phased mode, then combined with HPRC Phase 1 assemblies and +built into a variation graph with <a href="https://github.com/pangenome/pggb" target="_blank">pggb/Minigraph-Cactus</a>. +Bubbles in the graph were decomposed into variant records with +<a href="https://github.com/vcflib/vcflib" target="_blank">vcfwave</a>, +producing the source VCF used here. For this UCSC track, the decomposed +VCF was parsed, filtered to variants with an allele-length delta of at +least 50 bp, and collapsed by graph snarl ID (see the build documentation +linked below for details).</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>cpc1Sv</i>).</p> + +<p>For automated download, the bigBed files are at +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/cpc1.bb" target="_blank"> +http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/cpc1.bb</a> (native) and +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/cpc1.bb" target="_blank"> +http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/cpc1.bb</a> (lifted). +Use <tt>bigBedToBed</tt> to extract features: e.g. +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/cpc1.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p> + +<p>The original pangenome VCF is distributed by the Chinese Pangenome +Consortium; see the +<a href="https://github.com/Shuhua-Group/Chinese-Pangenome-Consortium-Phase-I" target="_blank"> +CPC Phase I repository</a>.</p> + +<h2>Credits</h2> + +<p>Thanks to the Chinese Pangenome Consortium and the HPRC Phase 1 team +for producing and releasing the combined pangenome and its decomposed +variant calls.</p> + +<h2>References</h2> + + +<p> +Gao Y, Yang X, Chen H, Tan X, Yang Z, Deng L, Wang B, Kong S, Li S, Cui Y <em>et al</em>. +<a href="https://doi.org/10.1038/s41586-023-06173-7" target="_blank"> +A pangenome reference of 36 Chinese populations</a>. +<em>Nature</em>. 2023 Jul;619(7968):112-121. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37316654" target="_blank">37316654</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322713/" target="_blank">PMC10322713</a> +</p> +