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>
+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,
+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>
+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>
+Items in all subtracks follow the same conventions: items are shaded according to variant type.
+<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.
+Mouseover on items indicates Allele Frequencies (AF).
+</p>
+
+<p> 
+All tracks can be filtered according to the <b>variant lenth</b> and <b>type of variant</b>. The
+<b>variant overlap</b> filter defines four bins within that range from which the user can choose.
+</p>
+ 
+
+<h2>Data Acces</h2>
+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>.
+</p>
+
+<p>
+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>
+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 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>
+