b4354dab1ce9929f4cd6b81628b545a3b0bd9840
dschmelt
  Wed Feb 26 14:43:22 2020 -0800
Adding note about bigDataIndex keyword #25018

diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html
index fe119c1..2db24c4 100755
--- src/hg/htdocs/goldenPath/help/vcf.html
+++ src/hg/htdocs/goldenPath/help/vcf.html
@@ -39,31 +39,37 @@
   <li>
   Create VCF or convert another format to VCF. Items must be sorted by genomic position.</li>
   <li>
   Compress your <em>.vcf</em> file using the <code>bgzip</code> program:
   <pre><code>bgzip my.vcf</code></pre>
   For more information about the <code>bgzip</code> command, run it with no arguments to
   display the usage message.</li>
   <li>
   Create a tabix index file for the bgzip-compressed VCF (<em>.vcf.gz</em>):
   <pre><code>tabix -p vcf my.vcf.gz</code></pre>
   The tabix command appends <em>.tbi</em> to the <em>my.vcf.gz</em> filename, creating a binary 
   index file named <em>my.vcf.gz.tbi</em> with which genomic coordinates can quickly be translated 
   into file offsets in <em>my.vcf.gz</em>.</li>
   <li>
   Move both the compressed VCF file (<em>my.vcf.gz</em>) and tabix index file 
-  (<em>my.vcf.gz.tbi</em>) to an http, https, or ftp location.</li>
+  (<em>my.vcf.gz.tbi</em>) to an http, https, or ftp location.Note that the Genome Browser
+  looks for an index file with the same URL as the VCF file with the .tbi suffix added. If your
+  hosting site does not use the filename as the URL link, you will have to specifically
+  call the location of this .vcf.tbi index file with the <code>bigDataIndex</code> keyword.
+  This keyword is relevant for Custom Tracks and Track Hubs. You can read more about 
+  <em>bigDataIndex</em> in
+  <a href="trackDb/trackDbHub.html#bigDataIndex">the TrackDb Database Definition page</a>.</li>
   <li>
   Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single 
   <a href="hgTracksHelp.html#TRACK">track line</a>. The basic version of the track line will look 
   something like this:
   <pre><code>track type=vcfTabix name="My VCF" bigDataUrl=<em>http://myorg.edu/mylab/my.vcf.gz</em></code></pre>
   Again, in addition to <em>http://myorg.edu/mylab/my.vcf.gz</em>, the associated index file 
   <em>http://myorg.edu/mylab/my.vcf.gz.tbi</em> must also be available at the same location.</li>
   <li>
   Paste the custom track line into the text box in the <a href="../../cgi-bin/hgCustom" 
   target="_blank">custom track management page</a>, click &quot;submit&quot; and view in the Genome 
   Browser.</li>
 </ol>
 
 <h2>Parameters for VCF custom track definition lines</h2>
 <p>