9d9210bb7b34131505ab50b5e62bb88680dc6129
mspeir
  Wed Sep 9 15:14:09 2026 -0700
trackDb docs: add vcfPhasedColorBy, refs #38010

vcfPhasedColorBy has been read by vcfUi.c since the trio display went in, but it
was documented nowhere: not on the VCF help pages, not in trackDbLibrary, and
tdbQuery -check would have rejected it because tagTypes.tab did not list it
either. So a hub author had no way to find the setting and no way to use it
without tripping the checker.

Add the library blurb, the rows in trackDbDoc.html and trackDbHub.v3.html, a
changes.html entry, and the tagTypes.tab registration. The blurb spells out that
mendelDiff needs vcfParentSamples and that function is only offered when
geneTrack is set, since both conditions are enforced in vcfUi.c and neither is
obvious from the value name.

Companion to the two commits documenting the same settings on vcf.html and
hgVcfTrackHelp.html.

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

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index cf2046dafa2..d707acee6bc 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -5198,30 +5198,44 @@
 <div class="vcfParentSamples"><span class="types vcfPhasedTrio"></span>
 <div class="format"><code>vcfParentSamples &lt;sampleName|altName,sampleName|altName&gt;</code></div>
     <P>
     A comma separated (no spaces) list of the VCF Genotype column IDs of the &quot;parents&quot;, followed optionally by a &quot;|&quot; character and an alias for the display. This setting is optinonal, and supports one or both parents.
     </P>
 </div>
 
 <DIV class="vcfUseAltSampleNames"><span class="types vcfPhasedTrio"></span>
 <div class="format"><code>vcfUseAltSampleNames &lt;on/off&gt;</code></div>
     <P>
     Make the display use the aliases as the default labels for each haplotype lane instead of the
     ID from the VCF.
     </P>
 </DIV>
 
+<DIV class="vcfPhasedColorBy"><span class="types vcfPhasedTrio"></span>
+<div class="format"><code>vcfPhasedColorBy &lt;mendelDiff|deNovo|function|noColor&gt;</code></div>
+    <P>
+    How to color the variants drawn on each haplotype lane. <code>noColor</code>, the default,
+    draws them all black. <code>deNovo</code> colors a child variant red when it appears in
+    neither parent. <code>mendelDiff</code> colors a child variant red when it disagrees with
+    the allele the parents imply was transmitted; this needs
+    <A HREF="#vcfParentSamples">vcfParentSamples</A> to be set. <code>function</code> colors by
+    predicted effect on the gene, red for non-synonymous, green for synonymous, blue for UTR or
+    noncoding, and black otherwise; it is offered only when
+    <A HREF="#geneTrack">geneTrack</A> is also set.
+    </P>
+</DIV>
+
 <DIV class="vcfPhasedTrio_example"><span class="types vcfPhasedTrio"></span>
 <div class="format"><B>Example of a VCF Phased Trio track</B></div>
     <pre>
     track myVcf
     type vcfPhasedTrio
     bigDataUrl http://myorg.edu/mylab/myVcf.gz
     vcfChildSample NA123456|son
     vcfParentSamples NA654321|mother,NA321654|father
     vcfUseAltSampleNames on
       ...    </pre>
     <P>The data for this VCF track is stored in the remote file,
     "myVcf.gz".  That file is paired with a tabix-generated index file named
     "myVcf.gz.tbi" found in the same remote location. "NA123456" is the ID of one
     of the Genotype columns in the VCF, and the parent haplotypes will displayed
     relative to their similarity to this sample.