c9814cbb9c9556663ee2cb8c9ea096a784582aac
dschmelt
  Fri Apr 19 16:48:30 2019 -0700
Adding a note about function of hap sort display as requested #22039

diff --git src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
index bf91342..45b4916 100755
--- src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
+++ src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
@@ -18,31 +18,32 @@
 <p class='text-center'>
   <img src="../../images/vcfDefault.png" alt="VCF default display" width=600px>
   <p class='gbsCaption text-center'>The default VCF custom track will display colored bases and 
 will not show clustering unless specified as VCF/tabix in the custom track page.</p>
 </p>
 <p>
 The following section describes configuration settings available to VCF files compressed and
 indexed in the Tabix format. This requires VCF manipulation, separate index files, and a web
 accessible directory to reference from the bigDataUrl track line. For more information
 on setting up and uploading VCF/Tabix data, click the link on <a href="vcf.html" target="_blank">
 VCF custom track creation</a>.
 </p>
 <h2>Configuring the haplotype sorting display</h2>
 <p>
 If the VCF file contains genotype columns for at least two samples (four haplotypes), then a 
-haplotype sorting display can be configured.</p> 
+haplotype sorting display can be configured. This can be useful for determining similarity
+between the samples and possible inheritance at a particular loci. </p> 
 <p>
 <strong>Enable Haplotype sorting display:</strong> When this option is checked, each sample's phased
 and/or homozygous genotypes are split into haplotypes, clustered by similarity around a central 
 variant, and sorted for display by their position in the clustering tree. The tree (as 
 space allows) is drawn in the label area next to the track image. Leaf clusters, in 
 which all haplotypes are identical (at least for the variants used in clustering), are 
 colored purple. 
 </p>
 <p class='text-center'>
   <img src="../../images/vcfTree.png" alt="VCF tree diagram" width=600px>
   <p class='gbsCaption text-center'>The haplotype tree can be seen to the left of the track.</p>
 </p>
 <p>
 Each variant is drawn as a vertical column, using color to distinguish between 
 reference alleles and alternate alleles of the horizontally running haplotypes. If unchecked, then