e6bcec351aa8f5bc7218e8862e15c149aadb3479 lrnassar Fri Jul 10 12:18:40 2026 -0700 lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged. diff --git src/hg/makeDb/trackDb/human/lrSvAll.html src/hg/makeDb/trackDb/human/lrSvAll.html index 1b97f6518c6..b12c1a8b655 100644 --- src/hg/makeDb/trackDb/human/lrSvAll.html +++ src/hg/makeDb/trackDb/human/lrSvAll.html @@ -1,81 +1,81 @@ <h2>Description</h2> <p> This track combines the structural-variant (SV) callsets from the individual -subtracks of the <a href="hgTrackUi?g=lrSv">Long-read SVs</a> supertrack into a +subtracks of the <a href="hgTrackUi?g=longReadVariants">Long-read SVs</a> supertrack into a single, position-merged overview. Each item is an SV locus seen in one or more of the contributing long-read databases. For every merged locus the track records which databases report it, the summed allele count across those databases, and the range of allele frequencies observed, making it useful for quickly seeing how widely an SV has been reported across cohorts. </p> <p> This is a summary view. For cohort-specific genotypes, per-population allele frequencies, and dataset-specific annotations, use the individual subtracks of the supertrack. The merge includes the released long-read callsets only; preliminary or unpublished subtracks (e.g. the Kim PD brain, 1000 Genomes linear, and HPRC Jasmine sets) are <b>not</b> part of this merged track. </p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV type, matching the individual subtracks: <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(0,160,0);">Duplications (DUP)</span> - green</li> <li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li> <li><span style="color: rgb(140,0,200);">Complex and other multi-allele events</span> - purple</li> </ul> </p> <p> The mouseover shows the variant name, SV type, reference and insertion lengths, the list of contributing source databases, the allele-frequency range across those databases, and the total allele count. Filters are available for the <b>source database</b>, <b>SV type</b>, <b>SV length</b>, <b>insertion length</b>, <b>total allele count</b>, <b>minimum and maximum allele frequency</b>, and the <b>number of source databases</b> reporting each locus. The detail page lists the per-database allele counts. </p> <h2>Methods</h2> <p> The merged track is built by the <tt>lrSvMergeAll.py</tt> script, which reads the bigBed of each contributing subtrack (configured in <tt>databases.tsv</tt>) and groups records that share an identical <tt>(chromosome, start, end)</tt> position and SV type. For each merged locus the script records the set of contributing databases (<tt>sources</tt>), the number of those databases (<tt>sourceCount</tt>), the sum of their allele counts (<tt>AC</tt>), and the minimum and maximum allele frequency across databases that report one (<tt>minAF</tt>, <tt>maxAF</tt>). The per-database allele counts are carried as additional columns. </p> <p> The step-by-step build commands are recorded in the UCSC makeDoc for this track collection: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank"> doc/hg38/lrSv.txt</a>. The merge script and autoSql schema live in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank"> makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSvAll.ra" target="_blank">trackDb/human/lrSvAll.ra</a>. </p> <h2>Data Access</h2> <p> The data can be explored interactively 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>lrSvAll</i>. </p> <p> The bigBed is available from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/lrSv/" target="_blank">our download server</a> as <tt>lrSvAll.bb</tt>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/lrSv/lrSvAll.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <h2>Credits</h2> <p> This merged view is derived entirely from the contributing long-read SV callsets; please see the individual subtrack description pages for the data producers and citations for each cohort. </p>