37adfded75ec133c1fd2b4cb86e4757e76a54de5
mspeir
  Wed Sep 9 15:29:55 2026 -0700
trackDb docs: describe minAc and vcfDoMinAc, and fix two mislabelled vcfDoMaf rows, refs #38010

The last two VCF settings with no description anywhere. Both were absent from
trackDbLibrary, trackDbDoc and trackDbHub.v3, so registering them in
tagTypes.tab last commit made them legal but still undiscoverable.

minAc is a real filter, not just a UI default: minAcFail() in vcfTrack.c takes
the largest alternate allele count from the AC field of the INFO column and
drops the record when it is below the setting. Records whose INFO has no usable
AC are never dropped, which is worth saying since it is the surprising half.
vcfDoMinAc gates the matching control, like its three siblings.

Rows follow the placement the sibling settings already use: minAc beside
minFreq in the vcfTabix table, vcfDoMinAc beside vcfDoMaf in both the vcfTabix
and vcfPhasedTrio tables.

While adding those, trackDbDoc.html turned out to carry two rows with
class="vcfDoMaf" whose anchor and format line both read vcfDoQual, so the page
listed vcfDoQual twice and never showed vcfDoMaf's syntax. Copy-paste, present
in both the vcfTabix and vcfPhasedTrio tables. Corrected.

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 d707acee6bc..17edd2e0d67 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -5094,50 +5094,65 @@
 <div class="format"><code>minQual &lt;<EM>Q</EM>&gt;</code></div>
     <P>
     <P>Assuming <code>applyMinQual</code> is <code>true</code>,
     this is the minimum QUAL value required for a variant to be displayed.
     </P>
 </DIV>
 
 <DIV class="minFreq"><span class="types vcf vcfTabix"></span>
 <div class="format"><code>minFreq &lt;<EM>F</EM>&gt;</code></div>
     <P>
     The minimum minor allele frequency required for a variant to be displayed.
     By default this is 0.0 (i.e. display all variants).
     </P>
 </DIV>
 
+<DIV class="minAc"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
+<div class="format"><code>minAc &lt;<EM>N</EM>&gt;</code></div>
+    <P>
+    The minimum alternate allele count required for a variant to be displayed, taken from the
+    AC field of the INFO column. Variants whose INFO has no usable AC are always displayed.
+    By default this is 0 (i.e. display all variants).
+    </P>
+</DIV>
+
 <DIV class="vcfDoFilter"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
 <div class="format"><code>vcfDoFilter &lt;on/off&gt;</code></div>
     <p>
     Turn on/off the FILTER options available by default for VCF tracks
     </p>
 </DIV>
 
 <DIV class="vcfDoQual"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
 <div class="format"><code>vcfDoQual &lt;on/off&gt;</code></div>
     <p>
     Turns on/off the QUAL filter options available by default for VCF tracks
     </p>
 </DIV>
 
 <DIV class="vcfDoMaf"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
 <div class="format"><code>vcfDoMaf &lt;on/off&gt;</code></div>
     <p>
     Turns on/off the Minor Allele Frequency filter options available by default for VCF tracks
     </p>
 </DIV>
+<DIV class="vcfDoMinAc"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
+<div class="format"><code>vcfDoMinAc &lt;on/off&gt;</code></div>
+    <p>
+    Turns on/off the minimum allele count filter option available by default for VCF tracks
+    </p>
+</DIV>
 
 <DIV class="sampleMetadataFile"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
 <div class="format"><code>sampleMetadataFile &lt;url&gt;</code></div>
     <P>
     Specifies a tab-separated file that provides metadata columns for VCF samples.
     (Meta data can always be provided in the VCF file directly, but this option
     allows storing the metadata in an external file.) 
     When a user clicks on a variant, the metadata columns from this file are appended
     to the genotype details table.
     The first line is a header that starts with <code>#sample</code>,
     followed by tab-separated column names for the metadata fields.
     Subsequent lines contain the sample name in the first column (matching
     the VCF genotype column IDs), followed by the metadata values.
     </P>
     <P>Example metadata file:</P>