6d02024d6f5b80437784b274ff2ccf6940dde976
mspeir
  Wed Sep 9 15:08:26 2026 -0700
VCF help: document geneTrack, the function coloring scheme, and vcfPhasedColorBy, refs #38010

The rest of the settings vcfUi.c reads from trackDb but neither help page
mentioned.

geneTrack (vcfUi.c:269 and :681) is the gate for the functional-effect coloring
in both the haplotype display and the trio display: the radio button is only
printed when the setting is non-empty. Nothing on either page said so, so the
scheme was undiscoverable and its absence looked like a bug.

hapClusterColorBy therefore has four values, not the three both pages listed --
hgVcfTrackHelp.html went as far as saying "There are three ways that reference
and alternate alleles can be colored" above three bullets. Add the fourth, in
the order vcfCfgHapClusterColor prints the buttons, and add function to the
value lists in vcf.html.

vcfPhasedColorBy (mendelDiff|deNovo|function|noColor) was documented nowhere at
all, not even in trackDbLibrary.shtml, though vcf.html already described what it
does in the alt text of the trio screenshot. Add it to the trio settings.

Both settings tables needed a wider value column to fit, so those rows are
repadded; no wording in them changed.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
index 989b0612616..c43cbaa81e9 100755
--- src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
+++ src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
@@ -59,42 +59,47 @@
 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 
 the display is the same as for VCF without genotypes: a stacked bar graph of the top two alleles, 
 showing the proportion of alleles if allele counts are available. This setting is enabled by 
 default.</p>
 
 <p>
 The following options are applicable only when the haplotype sorting display is enabled:</p>
 <p> 
 <strong>Haplotype sorting order:</strong> Haplotypes are sorted using a distance function that 
 uses a central variant. Differences between haplotypes are penalized with weights that decrease 
 for each successive variant away from the central variant.  By default, the median variant in 
 the window is used. By clicking on a variant in the display, you will get the option to always 
 use that variant when it is in the current view.</p>
 <p>
-<strong>Haplotype coloring scheme:</strong> There are three ways that reference and alternate 
+<strong>Haplotype coloring scheme:</strong> There are four ways that reference and alternate 
 alleles can be colored:</p>
 <ul>
   <li>
   By default, the reference allele is invisible and the alternate allele is black. When multiple
   haplotypes must be combined into the same pixel row, grayscale is used to shade according to 
   the proportions of reference and alternate alleles. The central variant has a thin purple 
   outline. Extra pixel rows at the top and bottom show the locations of variants in case they 
   are hard to see due when the invisible reference allele is the major allele. Variants used in 
   clustering have purple marks in these rows; variants outside the clustered regions have black 
   marks.</li>
   <li>
+  The reference allele is invisible and the alternate allele is colored by the effect it is
+  predicted to have on the gene: red for non-synonymous, green for synonymous, blue for UTR or
+  noncoding, and black otherwise. This option is offered only when the track has a
+  <strong>geneTrack</strong> setting naming the gene track to compare against.</li>
+  <li>
   The reference allele is blue and the alternate allele is red. Purple indicates a mix of 
   reference and alternate alleles. The central variant has a thick black outline.</li>
   <li>
   Both alleles are colored using the same color scheme as when there are no genotypes: A is 
   red, C is blue, G is green and T is magenta. Gray indicates a mix of reference and alternate 
   alleles. The central variant has a thick black outline.</li>
 </ul>
 <p>
 In all coloring modes, if some alleles in a haplotype are undefined, a pale yellowish color is 
 used for those alleles.</p>
 <p> 
 <strong>Haplotype clustering leaf shape:</strong> Leaf clusters are collections of identical 
 haplotypes. By default, they are drawn as open triangles &lt;. They can also be displayed as 
 open rectangles [.</p>