6cc1e1e4ce2f0553e9a45485279b6497e06a64e9
kuhn
  Thu Jan 7 17:09:44 2021 -0800
added a clarifyng phrase

diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html
index cb4135b..49fb004 100755
--- src/hg/htdocs/goldenPath/help/vcf.html
+++ src/hg/htdocs/goldenPath/help/vcf.html
@@ -18,31 +18,32 @@
 so large that the connection to UCSC would time out when attempting to upload the whole file to 
 UCSC. Both the VCF file and its tabix index file remain on your web-accessible server (http, https, 
 or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed
 up interactive display. If you do not have access to a web-accessible server and need hosting space
 for your VCF files, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the
 Track Hub Help documentation.</p>
 
 <p>The UCSC tools support VCF versions 3.3 and greater.</p>
 
 <p>If you have VCF trio data, you may be interested in formatting your track as a
 <a href="#trio">Phased Trios</a> track as described below.
 
 <h2>VCF Format </h2>
 <p>
 VCF is an all-purpose format for defining variants of all types: SNVs,
-CNVs and translocations.  It can annotate all the variants in an individual as well
+CNVs and translocations relative to a reference assembly.  It can annotate all the
+variants in an individual as well
 as a population.  Typically, a VCF file is too large to load directly into a custom
 track on the Browser and must be loaded as binary tabix-indexed file as described
 below.
 
 The full specification of VCF is found in
 <a href = "http://samtools.github.io/hts-specs/VCFv4.3.pdf" target = _blank>documents
 on github</a>.
 
 <p>Here is a look at an example from that file showing a few rows of data for
 three samples.  Details and descriptions of the data fields are in the
 <a href = "http://samtools.github.io/hts-specs/VCFv4.3.pdf" target = _blank>.pdf</a>.
 The data here can be pasted directly into hg18 human assembly on the Genome Browser.  We
 have added two lines at the top of the entry that are not in the official example
 to make the display work in the Browser.
 </p>