9923b0d727379c208d267d367c59ca69829a0b94
max
  Tue Dec 17 04:21:56 2024 -0800
adding spliceImpact super track and splicevardb track under it, refs #34424

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+<h2>Description</h2>
+
+<p>
+The "Splicing Impact" container track contains tracks showing the predicted or validated effect of variants
+close to splice sites.
+</p>
+
+<h3>SpliceVarDB</h3>
+<p>SpliceVarDB is an online database consolidating over 50,000 variants assayed
+for their effects on splicing in over 8,000 human genes. The authors evaluated
+over 500 published data sources and established a spliceogenicity scale to
+standardize, harmonize, and consolidate variant validation data generated by a
+range of experimental protocols. The database is available at 
+<a target=_blank href="https://splicevardb.org">splicevardb.org</a>.</p>
+
+<h2>Display Conventions and Configuration</h2>
+
+<h3>SpliceVarDB</h3>
+<p>According to the strength of their supporting
+evidence, variants were classified as "splice-altering" (∼25%), "not
+splice-altering" (∼25%), and "low-frequency splice-altering" (∼50%), which
+correspond to weak or indeterminate evidence of spliceogenicity. 55% of the
+splice-altering variants in SpliceVarDB are outside the canonical splice sites
+(5.6% are deep intronic). The data is shown as lollipop plots that can be clicked, 
+the details page then shows a link to SpliceVarDb with full details.
+</p>
+
+<h2>Data Access</h2>
+<p>
+The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>
+or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. The data can be
+accessed from scripts through our <a href="https://api.genome.ucsc.edu">API</a>, the track name is
+"splicevardb".
+
+<p>
+For automated download and analysis, the genome annotation is stored in a bigBed file that
+can be downloaded from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/splicevardb/" target="_blank">our download server</a>.
+The file for this track is called <tt>SVADB.bb</tt>. Individual
+regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>
+which can be compiled from the source code or downloaded as a precompiled
+binary for your system. Instructions for downloading source code and binaries can be found
+<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
+The tool
+can also be used to obtain only features within a given range, e.g. 
+<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/splicevardb/SVADB.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p>
+</p>
+
+</p>
+
+<h2>Methods</h2>
+<p>The data was converted by Patricia Sullivan from SpliceVarDb within a few
+hours to bigLolly format and the UCSC Browser staff needed nothing else to do but to downloaded the data.  </p>
+
+<h2>Credits</h2>
+<p>Thanks to the SpliceVarDB team for converting the data into our data formats.</p>
+
+<h2>References</h2>
+<p>
+Sullivan PJ, Quinn JMW, Wu W, Pinese M, Cowley MJ.
+<a href="https://linkinghub.elsevier.com/retrieve/pii/S0002-9297(24)00288-X" target="_blank">
+    SpliceVarDB: A comprehensive database of experimentally validated human splicing variants</a>.
+<em>Am J Hum Genet</em>. 2024 Oct 3;111(10):2164-2175.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39226898" target="_blank">39226898</a>; PMC: <a
+    href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480807/" target="_blank">PMC11480807</a>
+</p>