65091fe6f6487c23d650a144e947fc1c582d3f40 max Tue Apr 21 02:16:16 2026 -0700 abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376 diff --git src/hg/makeDb/trackDb/human/hg38/abelSv.html src/hg/makeDb/trackDb/human/abelSv.html similarity index 91% rename from src/hg/makeDb/trackDb/human/hg38/abelSv.html rename to src/hg/makeDb/trackDb/human/abelSv.html index 82cd0ab81b5..7d5913fffb5 100644 --- src/hg/makeDb/trackDb/human/hg38/abelSv.html +++ src/hg/makeDb/trackDb/human/abelSv.html @@ -1,47 +1,51 @@ <h2>Description</h2> <p> Structural variants (SVs) are large changes in DNA — deletions, duplications, inversions, insertions of mobile elements, and translocations — that are at least 50 base pairs in size. They are a major source of genetic variation between individuals and can affect gene dosage, disrupt coding sequence, or rearrange regulatory elements. Because SVs are harder to detect than small variants, population-scale SV maps lag behind single-nucleotide variant resources.</p> <p> -This track displays site-frequency data for 738,624 SVs identified in 17,795 -deeply sequenced human genomes (mean coverage > 20×) by +This track displays site-frequency data for 737,998 SVs identified in 17,795 +deeply sequenced human genomes (mean coverage > 20×) by Illumina +short-read sequencing by <a href="https://www.nature.com/articles/s41586-020-2371-0" target="_blank"> Abel et al., Nature 2020</a>. The samples were sequenced by the four sequencing centers of the NHGRI <a href="https://www.genome.gov/Funded-Programs-Projects/NHGRI-Genome-Sequencing-Program/Centers-for-Common-Disease-Genomics" target="_blank"> Centers for Common Disease Genomics (CCDG)</a> program, supplemented with ancestrally diverse samples from the PAGE consortium and the Simons Genome Diversity Project. The composition includes roughly 24% African, 16% Latino, 11% Finnish, 39% non-Finnish European, and 9% other ancestries.</p> <p> -Two non-overlapping public callsets are displayed as a single track:</p> +Two non-overlapping public callsets are combined into this track. +The upstream release contains 738,624 unique primary SV records across +the two callsets; 626 B37 records did not lift over to GRCh38, leaving +the 737,998 shown here:</p> <ul> - <li><b>B38</b> (native GRCh38): 14,623 samples, called directly on the - GRCh38 assembly.</li> - <li><b>B37lift</b> (GRCh37, lifted): 8,417 samples originally called on - GRCh37, with coordinates lifted to GRCh38 using the standard UCSC - hg19→hg38 liftOver chain. 626 variants could not be lifted.</li> + <li><b>B38</b> (native GRCh38): 458,106 SVs from 14,623 samples, called + directly on the GRCh38 assembly.</li> + <li><b>B37lift</b> (GRCh37, lifted): 279,892 SVs from 8,417 samples + originally called on GRCh37, with coordinates lifted to GRCh38 + using the standard UCSC hg19→hg38 liftOver chain.</li> </ul> <p> <b>Important:</b> the B38 and B37 callsets share 5,245 samples. When inspecting a variant present in both callsets, users should not simply sum the allele counts; the AC/AN reported for each callset reflects that callset's sample set. The <i>callset</i> filter can be used to restrict display to one source.</p> <h2>Display conventions</h2> <p>Items are colored by SV type:</p> <ul> <li><span style="background-color:rgb(220,50,32);color:white;padding:1px 6px">DEL</span> deletion</li> <li><span style="background-color:rgb(0,120,200);color:white;padding:1px 6px">DUP</span> duplication</li> <li><span style="background-color:rgb(230,140,0);color:white;padding:1px 6px">INV</span> inversion</li>