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/srSv.html src/hg/makeDb/trackDb/human/srSv.html index 252ace3e465..caccfd8b171 100644 --- src/hg/makeDb/trackDb/human/srSv.html +++ src/hg/makeDb/trackDb/human/srSv.html @@ -1,105 +1,105 @@ <h2>Description</h2> <p> This track collection contains structural variant (SV) and copy-number variant (CNV) callsets derived from Illumina <b>short-read</b> sequencing. Most SV tracks in the browser now come from long-read platforms (see the companion -<a href="hgTrackUi?g=lrSv">Long-read SVs</a> supertrack); the short-read +<a href="hgTrackUi?g=longReadVariants">Long-read SVs</a> supertrack); the short-read callsets here are included as comparators so users can evaluate the extra sensitivity of long-read calls and cross-check a variant across technologies. </p> <h3>Available Datasets</h3> <p> SV length statistics (min / median / max) are computed from the <tt>svLen</tt> field of each track, in base pairs. For the Abel CCDG callset, a large fraction of records are breakend (BND) translocations where <tt>svLen=-1</tt> is used as a sentinel, which shows up in both min and median. </p> <table class="stdTbl"> <tr> <th>Dataset</th> <th>N samples</th> <th>Cohort / disease</th> <th>Sequencing</th> <th>SVs</th> <th>Min</th> <th>Median</th> <th>Max</th> </tr> <tr> <td><a href="hgTrackUi?g=abelSv">CCDG 17,795</a></td> <td>17,795</td> <td>NHGRI CCDG + PAGE + SGDP (B38 native + B37 lifted)</td> <td>Illumina short-read (LUMPY + CNVnator + svtyper)</td> <td>737,998</td> <td>-1</td> <td>-1</td> <td>217,985,413</td> </tr> <tr> <td><a href="hgTrackUi?g=onekg3202Sr">1KG 3202</a></td> <td>3,202</td> <td>1000 Genomes expanded cohort</td> <td>Illumina short-read (GATK-SV)</td> <td>173,366</td> <td>1</td> <td>314</td> <td>154,807,729</td> </tr> <tr> <td><a href="hgTrackUi?g=tommoJpCnv">ToMMo 48K CNV</a></td> <td>48,874</td> <td>Japanese, general population</td> <td>Illumina short-read (GATK CNV, 1 kb bins, shown as two bigWigs)</td> <td colspan="4">~2M bins with CNV carriers; not comparable to per-SV counts above</td> </tr> </table> <h3>CCDG 17,795 SVs (<a href="hgTrackUi?g=abelSv">abelSv</a>)</h3> <p> Site-frequency callset from 17,795 deeply sequenced genomes (Abel et al. 2020, Nature; PMID 32460305). Two non-overlapping public releases are combined in this track: the B38 callset (14,623 samples called natively on GRCh38) and the B37 callset (8,417 samples, lifted). Variants are colored by SV type (DEL / DUP / INV / MEI / BND) and carry per-population allele counts for eight ancestry groups plus a HIGH/LOW confidence filter. </p> <h3>1KG 3202 SVs (<a href="hgTrackUi?g=onekg3202Sr">onekg3202Sr</a>)</h3> <p> 1000 Genomes 3202-sample Illumina short-read GATK-SV callset (Byrska-Bishop et al. 2022). 173,366 SVs across 7 classes (DEL, INS, DUP, INV, CPX, CNV, CTX) with AC/AN/AF and per-superpopulation AFs (AFR/AMR/ASN/EUR/SAN). </p> <h3>ToMMo 48K CNV SR (<a href="hgTrackUi?g=tommoJpCnv">tommoJpCnv</a>)</h3> <p> Per-1 kb-bin copy-number carrier counts from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 48KJPN-CNV Frequency Panel, release 20230828), called with GATK CNV germline workflows. Shown as a multiWig overlay: red = samples with copy-number loss (CN<2) per bin, green = samples with gain (CN>2) per bin. This is a useful short-read point of comparison to the ToMMo 333-sample long-read SV track under the Long-read SVs supertrack. </p> <h2>Data Access</h2> <p> See the Data Access section of each subtrack's page for download links. Build documentation lives alongside the scripts at <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/srSv.txt" target="_blank"> doc/hg38/srSv.txt</a>; conversion scripts and autoSql schemas are at <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/srSv" target="_blank"> makeDb/scripts/srSv</a>. </p> <h2>Credits</h2> <p> Each subtrack credits its respective upstream project; see the individual description pages. </p> <h2>References</h2> <p> See the individual subtrack description pages for the specific references. </p>