4a819ccfe7f5074c2295daacd838731fe59534fb
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  Tue Sep 17 02:16:07 2019 -0700
new avada track, refs #24156

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+<h2>Description</h2>
+
+<p>
+This track shows the genomic positions of variants in the
+<a href="http://bejerano.stanford.edu/AVADA/" target="_blank">AVADA database</a>. 
+AVADA is a database of variants built by a machine learning software
+that analyzes full text research articles to find the gene mentions in the text that 
+look like they are most relevant for genetic diagnosis, finds variant descriptions
+and uses the genes to map the variants to the genome. For details see the 
+<a target=_blank href="https://doi.org/10.1038/s41436-019-0643-6">AVADA paper</a>.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+
+<p>
+Genomic locations of a variants are labeled with the variant description
+in the original next. This is not a normalized HGVS string, but the original
+text as the authors of the study described it.
+The Pubmed ID, gene and transcript for each variant are shown on the
+variant's details page.
+</p>
+
+<H2>Data access</H2>
+<p>
+The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>,
+for download, intersection or correlations with other tracks. To join this track with others
+based on the chromosome positions, use the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>.
+
+<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/bbi/" target="_blank">our download server</a>.
+The files for this track are called <tt>clinVarMain.bb</tt> and <tt>clinVarCnv.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/bbi/clinvar/clinvarMain.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p>
+</p>
+
+<p>
+For automated access, this track like all others, is also available via our <a href="https://api.genome.ucsc.edu">API</a>.
+However, for bulk processing in pipelines, downloading the data and/or using bigBed files as described above is usually faster.
+</p>
+
+<h2>Methods</h2>
+
+<p>
+The AVADA VCF file was reformatted at UCSC to the <a href="../goldenPath/help/bigBed.html">bigBed</a> format.
+The program that performs the conversion is available on
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/avada"
+target="_blank">Github</a>.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to Gill Bejerano and Johannes Birgmeier for making the data available.
+</p>
+
+<h2>References</h2>
+<p>
+Johannes Birgmeier, Cole A. Deisseroth, Laura E. Hayward, Luisa M. T. Galhardo, Andrew P. Tierno, Karthik A. Jagadeesh, Peter D. Stenson, David N. Cooper, Jonathan A. Bernstein, Maximilian Haeussler, and Gill Bejerano:
+<em>et al</em>.
+<a href="https://doi.org/10.1038/s41436-019-0643-6" target="_blank">
+AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature. </a>.
+<em>Genetics in Medicine</em>. 2019.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31467448" target="_blank">31467448</a>
+</p>