da43847aab52991e91bfec700b16038710710038
max
  Sat Sep 26 21:56:05 2026 -0700
VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index 77fa9a20c91..6c2f752faa9 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -5208,30 +5208,41 @@
     <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="excludeFilterValues"><span class="types vcf vcfTabix vcfPhasedTrio"></span>
+<div class="format"><code>excludeFilterValues &lt;<EM>value1,value2,...</EM>&gt;</code></div>
+    <P>
+    A comma-separated list of values of the VCF FILTER column. Variants with any of these
+    values are hidden by default. The values must be defined in the VCF header; they are
+    shown pre-checked in the "Exclude variants with these FILTER values" list on the track
+    configuration page, where the user can uncheck them. By default nothing is excluded.
+    </P>
+    <P>Example: <code>excludeFilterValues NonHumanIns</code></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>