bac95a147f49cd331052e597006e04b3deee40fc max Wed Apr 22 10:43:20 2026 -0700 lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258 diff --git src/hg/makeDb/trackDb/human/tommoJpSv.html src/hg/makeDb/trackDb/human/tommoJpSv.html index 10c3117337e..91d181cf572 100644 --- src/hg/makeDb/trackDb/human/tommoJpSv.html +++ src/hg/makeDb/trackDb/human/tommoJpSv.html @@ -1,103 +1,132 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) identified by Oxford Nanopore long-read sequencing of 333 Japanese individuals from the Tohoku Medical Megabank (ToMMo) project. The 333 individuals form 111 parent-offspring trios, enabling Mendelian consistency checks on the SV calls. Activated T lymphocytes were used as a source of high-molecular-weight DNA for nanopore sequencing at a median coverage of 22.2x with an N50 read length of 25.8 kb. </p> <p> The dataset contains 74,201 SVs (37,981 deletions and 36,220 insertions), merged across individuals using SURVIVOR v1.0.6. Over 95% of the SVs are concordant with Mendelian inheritance in the trio families. </p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV type: <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> </ul> </p> <p> Filters are available for SV type, SV length, and allele frequency. For insertions, the item is placed at the insertion site with a width of 1 bp; for deletions, the item spans the deleted region. </p> <p> The detail page for each item shows: <ul> <li><b>Allele Frequency</b>: fraction of alleles carrying this variant (based on 444 alleles from 222 unrelated parents)</li> <li><b>Allele Count / Allele Number</b>: number of variant alleles and total alleles genotyped</li> <li><b>Mendelian Error Rate</b>: fraction of trio families showing inheritance errors for this variant</li> <li><b>Families with Errors / Families Genotyped</b>: number of families with Mendelian errors and total families with complete genotype calls</li> </ul> </p> <h2>Methods</h2> <p> Otsuki et al. 2022 extracted high-molecular-weight genomic DNA from activated T lymphocytes of 333 individuals (111 parent-offspring trios) from the Tohoku Medical Megabank (ToMMo) BirThree cohort and performed Oxford Nanopore whole-genome sequencing on PromethION instruments with R9.4.1 flow cells (SQK-LSK109 libraries, Guppy v4.2.2 high-accuracy base-calling). After QC, median per-sample sequencing coverage was 22.2x with a read N50 of 25.8 kb. Reads were aligned to GRCh38 with LRA, SVs were called per sample with <a href="https://github.com/tjiangHIT/cuteSV" target="_blank">CuteSV</a> v1.0.9 (<tt>-min_sv_length 50</tt>), and per-sample calls were merged with <a href="https://github.com/fritzsedlazeck/SURVIVOR" target="_blank">SURVIVOR</a> v1.0.6 (1000 bp distance, type-match, no length-match) into a nonredundant panel of 74,201 autosomal SVs (37,981 deletions and 36,220 insertions). Over 95% of the SVs were concordant with Mendelian inheritance in the 111 trio families; allele frequencies in this track are computed from the 222 unrelated parents to avoid double-counting. </p> <p> The site-only VCF <tt>tommo-JSV1-20211208-GRCh38-without-genotype-count.vcf.gz</tt> -was downloaded from the jMorp JSV1 dataset page, -<a href="https://jmorp.megabank.tohoku.ac.jp/datasets/tommo-jsv1-20211208-af" target="_blank"> +was downloaded from the jMorp JSV1 download page, +<a href="https://jmorp.megabank.tohoku.ac.jp/downloads/tommo-jsv1-20211208-af" target="_blank"> tommo-jsv1-20211208-af</a>. </p> <p> The step-by-step build commands (download, format conversion, 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> Source data is available from the -<a href="https://jmorp.megabank.tohoku.ac.jp/downloads" - target="_blank">jMorp downloads page</a> (ToMMo Japanese Multi Omics Reference Panel). +<a href="https://jmorp.megabank.tohoku.ac.jp/downloads/tommo-jsv1-20211208-af" + target="_blank">tommo-jsv1-20211208-af download page</a> on the jMorp +portal (ToMMo Japanese Multi Omics Reference Panel). +</p> + +<h2>Conditions of Use</h2> +<p> +The information in the ToMMo jMorp database is provided only to persons +who agree to jMorp's +<a href="https://jmorp.megabank.tohoku.ac.jp/help/conditions-of-use" target="_blank"> +Conditions of Use</a>. By using these data, you are deemed to have read +and understood those conditions and to agree to the following obligations: +<ul> +<li>Do not attempt to identify or contact any person who provided specimens +used to construct the information.</li> +<li>Request permission from dist [AT] megabank [DOT] tohoku [DOT] ac [DOT] jp +prior to using the data for commercial purposes.</li> +<li>Notify dist [AT] megabank [DOT] tohoku [DOT] ac [DOT] jp when providing +re-edited data to any third party.</li> +<li>Cite the jMorp paper in publications that report analyses based on +these data: Tadaka S, Kawashima J, Hishinuma E, <i>et al.</i>, +“jMorp: Japanese Multi-Omics Reference Panel update report 2023”, +<i>Nucleic Acids Research</i>, 2023 Nov 1, +<a href="https://doi.org/10.1093/nar/gkad978" target="_blank">doi:10.1093/nar/gkad978</a>; +please also refer to the per-dataset citation notes linked from that page.</li> +</ul> +The copyright in the information and the database is owned by ToMMo. If a +dataset-specific contact or Data Transfer Agreement is attached to a given +dataset, those should be followed in preference to this generic page. +Questions should be directed to +tommo-jmorp [AT] grp [DOT] tohoku [DOT] ac [DOT] jp. </p> <h2>Credits</h2> <p> Thanks to the Tohoku Medical Megabank Organization for making their structural variant calls publicly available through the jMorp data portal. </p> <h2>References</h2> <p> Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S <em>et al</em>. <a href="https://doi.org/10.1038/s42003-022-03953-1" target="_blank"> Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long- read sequencing technology</a>. <em>Commun Biol</em>. 2022 Sep 20;5(1):991. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36127505" target="_blank">36127505</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9489684/" target="_blank">PMC9489684</a> </p>