3e1960b35a07377b46bd83b8fd04387f182c6bd6
abenetpa
  Fri May 15 10:52:51 2020 -0700
added three description pages for dbVar tracks refs #25424

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+<h2>Description</h2>
+<p>
+The tracks listed here contain data from the
+<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/var_summary/#nstd186">
+nstd186 (NCBI Curated Common Structural Variants)</a> study. This is a collection of structural
+variants (SV) originally submitted to dbVar which are part of a study with at least 100 samples and
+have an allele frequency of &gt;=0.01 in at least one population. The complete dataset is imported
+from these common-population studies:
+</p>
+
+<p>
+<b>gnomAD Structural Variants</b>
+<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd166/">(nstd166)</a>:
+ Catalog of SVs detected from the sequencing of the complete genome of 10,847 unrelated
+individuals from the GnomAD v2.1 release.</p>
+<p>
+<b>1000 Genomes Consortium Phase 3 Integrated SV</b>
+<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/estd219/">(estd219)</a>:
+ Structural variants of the 1000 Genomes project Phase 3 as reported in a separate article
+specifically dedicated to the analysis of SVs. Many of these data are identical to those reported
+in the <a target=_blank 
+href="https://www.ncbi.nlm.nih.gov/dbvar/studies/estd214/">estd214</a> study.</p>
+<p>
+<b>DECIPHER Common CNVs</b>
+<a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd183/">(nstd183)</a>:
+Consensus set of common population CNVs selected from high-resolution controls sets where frequency
+information is available.
+</p>
+
+<p>
+There are two tracks in this collection:
+<ul>
+<li><a href="/cgi-bin/hgTrackUi?hgsid=395092309_WCeXo2V0Ug6yJ1KducDbjPkMSade&c=chr1&g=dbVar_common">
+<b>NCBI dbVar Curated Common Structural Variants (dbVar Common SV)</b></a>: Shows copy number
+variants calls (variants &gt;=50 nucleotides) from the <a target=_blank 
+href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186</a> study.</li>
+<li><a href="/cgi-bin/hgTrackUi?hgsid=395092309_WCeXo2V0Ug6yJ1KducDbjPkMSade&c=chr1&g=dbVar_conflict">
+<b>NCBI dbVar Curated Conflict Variants (dbVar Conflict SV)</b></a>: Shows copy number
+variants from <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186</a>
+(NCBI Curated Common Structural Variants) that overlap with
+<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd102/">nstd102</a> (Clinical
+Structural Variants).</li>
+</ul>
+</p>
+
+<h2>Display Conventions</h2>
+<p>
+These tracks are multi-view composite tracks that contain multiple data types (views). Each view
+within a track has separate display controls, as described
+<a href="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>. Some dbVar tracks
+contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks,
+only some subtracks will be displayed by default. The user can select which subtracks are displayed
+via the display controls on the track details page.
+</p>
+
+<h2>Data Acces</h2>
+<p>
+The raw data can be explored interactively with the
+<a href="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a>, or the
+<a href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis,
+the data may be queried from our
+<a href="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>. The data can also be found
+directly from the dbVar nstd186 <a target=_blank 
+href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/#data_access">data access</a>.
+For questions about dbVar track data, please contact <em>dbvar@ncbi.nlm.nih.gov</em>.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to the dbVAR team at NCBI, especially Timothy Hefferon for technical coordination and
+consultation, and to Christopher Lee, Anna Benet-Pages, and Maximilian Haeussler of the Genom 
+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>
+