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) diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index 835ac8a5d49..96a3db50264 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -1380,39 +1380,45 @@

minFreq <F>

+ +

minAc <N>

vcfDoFilter <on/off>

vcfDoQual <on/off>

vcfDoMaf <on/off>

+ +

vcfDoMinAc <on/off>

sampleMetadataFile <url>

Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks.

maxWindowCoverage maxWindowToDraw

Example of a VCF track