b82ec846ffc1bbe552cdc84cc439232f9cd6f04c
gperez2
  Tue Mar 7 18:08:31 2023 -0800
Adding Data Access section to description pages, refs #25566

diff --git src/hg/makeDb/trackDb/human/dgv.html src/hg/makeDb/trackDb/human/dgv.html
index 55d37df..2530c60 100644
--- src/hg/makeDb/trackDb/human/dgv.html
+++ src/hg/makeDb/trackDb/human/dgv.html
@@ -71,30 +71,49 @@
 A brief description of the method and sample used for a particular 
 variant is included on the details page, along with a link to the 
 PubMed abstract for the study from which the variants were collected.  
 </P>
 <P>
 For data sets where the variation calls are reported at a 
 sample-by-sample level, DGV merges calls with similar boundaries 
 across the sample
 set. Only variants of the same type (i.e. CNVs, Indels, inversions)
 are merged, and gains and losses are merged separately.  In addition,
 if several different platforms/approaches are used within the same
 study, these datasets are merged separately. Sample level calls that
 overlap by &ge; 70% are merged in this process.
 </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 access, this track, like all
+others, is available via our <a href="../goldenPath/help/api.html">API</a>. However, for bulk
+processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed
+file that can be downloaded from the
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/">download server</a>.
+The exact filenames can be found in the track configuration file. Annotations can be converted to
+ASCII text by our tool <code>bigBedToBed</code> 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, for example:</p>
+
+<pre>
+bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gnomAD/structuralVariants/gnomad_v2.1_sv.sites.bb -chrom=chr6 -start=0 -end=1000000 stdout
+</pre>
+
 <H2>Credits</H2>
 <P>
 Thanks to the <A HREF="http://dgvbeta.tcag.ca/dgv/app/home" 
 TARGET=_BLANK>Database of Genomic Variants</A> for providing these data.
 In citing the Database of Genomic Variants please refer to Iafrate 
 <em>et al.</em>.  
 </P>
 
 <H2>References</H2>
 <P>
 Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y,
 Scherer SW, Lee C.
 <A HREF="https://www.ncbi.nlm.nih.gov/pubmed/15286789" 
 TARGET=_BLANK>Detection of large-scale variation in the human genome</A>.
 <em>Nat Genet.</em> 2004 Sep;36(9):949-51. PMID:15286789.</P>