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/dgvPlus.html src/hg/makeDb/trackDb/human/dgvPlus.html
index 71440f3..74caf39 100644
--- src/hg/makeDb/trackDb/human/dgvPlus.html
+++ src/hg/makeDb/trackDb/human/dgvPlus.html
@@ -108,30 +108,49 @@
 <A HREF="https://www.ncbi.nlm.nih.gov/dbvar/" TARGET=_BLANK>dbVar</A> and
 <A HREF="https://www.ebi.ac.uk/dgva" TARGET=_BLANK>DGVa</A>.
 DGV then applies <a href="http://dgv.tcag.ca/dgv/app/faq#q4"
 target="_blank">quality filters</a> and merges overlapping variants.
 </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.
 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 https://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/dgvMerged.bb  -chrom=chr6 -start=0 -end=1000000 stdout
+</pre>
+
 <H2>Credits</H2>
 <P>
 Thanks to the <A HREF="http://dgv.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 MacDonald
 <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.nature.com/articles/ng1416" target="_blank">
 Detection of large-scale variation in the human genome</a>.
 <em>Nat Genet</em>. 2004 Sep;36(9):949-51.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15286789" target="_blank">15286789</a>