b85c12cf9af0ee1a954b8cced961bcbd909b7979 lrnassar Wed Apr 29 12:04:36 2026 -0700 Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree. diff --git src/hg/makeDb/trackDb/human/dbVarConflict.html src/hg/makeDb/trackDb/human/dbVarConflict.html index d509497b5c9..3e5dd4038f4 100644 --- src/hg/makeDb/trackDb/human/dbVarConflict.html +++ src/hg/makeDb/trackDb/human/dbVarConflict.html @@ -1,82 +1,91 @@ <h2>Description</h2> +<p> The track <b>NCBI dbVar Curated Common SVs: Conflicts with Pathogenic</b> highlights loci where common copy number variants from <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186 (NCBI Curated -Common Structural Variants)</a> overlap with structural Variants with clinical assertions, +Common Structural Variants)</a> overlap with structural variants with clinical assertions, submitted to ClinVar by external labs <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/var_summary/#nstd102">(Clinical Structural Variants - nstd102)</a>. </p> <p> <em>Overlap</em> in the track refers to reciprocal overlap between variants in the <b><em>common</em> -(NCBI Curated Common Structural Variants)</b> versus <b><em>clinical</em> (ClinVar Long Variants)</b> +(NCBI Curated Common Structural Variants)</b> versus <b><em>clinical</em> (ClinVar CNVs)</b> tracks. Reciprocal overlap values can be anywhere from 10% to 100%. </p> <p> For more information on the number of variant calls and latest statistics for nstd186 see <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/">Summary of nstd186</a> (NCBI Curated Common Structural Variants). </p> <h2>Display Conventions and Configuration</h2> <p> -Items in all subtracks follow the same conventions: items are colored by variant type, and are -based on the dbVar colors described in the +Items in this track follow the same conventions as the parent Common SV track: items are colored +by variant type, based on the dbVar colors described in the <a target="_blank" href="https://www.ncbi.nlm.nih.gov/dbvar/content/overview/">dbVar Overview page</a>. -<b><font color="red">Red</font></b> for copy number loss or deletion, -<b><font color="blue">blue</font></b> for copy number gain or duplication, and -<b><font color="#662180">violet</font></b> for copy number variation. +The variant types present in this track are copy number gain, copy number loss, copy number +variation, deletion, and duplication. </p> +<table> +<thead><tr> +<th style="border-bottom: 2px solid #6678B1;">Color</th> +<th style="border-bottom: 2px solid #6678B1;">Variant Type(s)</th> +</tr></thead> +<tbody> +<tr><th bgcolor="#ff0000"></th><td>copy number loss, deletion</td></tr> +<tr><th bgcolor="#0000ff"></th><td>copy number gain, duplication</td></tr> +<tr><th bgcolor="#4f1c73"></th><td>copy number variation</td></tr> +</tbody> +</table> <p> <b>Mouseover</b> on items indicates genes affected, size, variant type, and allele frequencies (AF). All tracks can be filtered according to the <b>variant length</b>, <b>variant type</b> and -<b>variant overlap</b>. This last filter defines four bins within that range from which the -user can choose. +<b>variant overlap</b>. The overlap filter defines five bins within that range (10-25, +25-50, 50-75, 75-90, 90-100 percent reciprocal overlap; intervals are inclusive of the upper bound). </p> <h2>Data Access</h2> +<p> The raw data can be explored interactively with the <a href="hgTables">Table Browser</a>, or the <a href="hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our -<a href="../../goldenPath/help/api.html">REST API</a>. </p> +<a href="../../goldenPath/help/api.html">REST API</a>. +</p> <p> The data can also be found directly from the <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/#data_access">dbVar nstd186 data access</a>, as well as in the <a href="hgHubConnect?hubUrl= https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt&hgHub_do_redirect=on"> dbVar Track Hub</a>, where additional subtracks are included. For questions about -dbVar track data, please contact <A HREF="mailto:dbvar@ncbi. -nlm. -nih. -gov"> -dbvar@ncbi. -nlm. -nih. -gov</A>. +dbVar track data, please contact +<A HREF="mailto:dbvar@ncbi.nlm.nih.gov">dbvar@ncbi.nlm.nih.gov</A>. <!-- above address is dbvar at ncbi.nlm.nih.gov --> </p> -Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical +<h2>Credits</h2> +<p> +Thanks to the dbVar team at NCBI, especially John Lopez and Timothy Hefferon for technical coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of the Genome Browser team for engineering the track display. </p> <h2>References</h2> <p> Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G <em>et al</em>. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gks1213" target="_blank"> DbVar and DGVa: public archives for genomic structural variation</a>. <em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D936-41. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193291" target="_blank">23193291</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531204/" target="_blank">PMC3531204</a> </p>