af9a5b388259e680dd34bc47b2cad4ff6e3d162f
lrnassar
  Sat Jun 13 03:00:51 2026 -0700
varFreqs: pre-release polish from comprehensive sanity check.

* Sync the new combined-track shortLabels into the four description pages:
"Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected"
-> "Population reference" (matches the trackdb shortLabels users now see).
* Add a paragraph in the supertrack Methods section describing the pooled
affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an
configuration that handles AF-only cohorts.
* Update the in-track Methods paragraphs on varFreqsAffected.html and
varFreqsBackground.html: replace "summed/maximized" with "pooled".
* Fix supertrack table downloadability column to match the underscore-prefix
convention: allofus "Yes" -> "No" (description page already says license
restricted); gregor "No" -> "Yes" (description page says VCF is on our
download server, and the gbdb path is not underscore-prefixed).
* Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the
default_an mechanism, the new affectedAN/backgroundAN columns, the
before/after spot-check at APOE rs429358, and the build commands.

refs #36642

diff --git src/hg/makeDb/trackDb/human/varFreqsArray.html src/hg/makeDb/trackDb/human/varFreqsArray.html
index da0c5f25410..b92b7fb5a94 100644
--- src/hg/makeDb/trackDb/human/varFreqsArray.html
+++ src/hg/makeDb/trackDb/human/varFreqsArray.html
@@ -1,28 +1,28 @@
 <h2>Description</h2>
 <p>
 This track merges variants from three genotyping-array cohorts into a single bigBed file
 with predicted protein consequences and cross-database filtering. It contains 14.7 million
 variants from the Taiwan Precision Medicine Initiative (TPMI Axiom TPM1 chip,
 ~1 million Han Chinese), the Mexico Biobank (MexBB, 6,011 individuals), and UK Biobank
 (361k unrelated white British, imputed from the Neale Lab Round 2 release).
 </p>
 
 <p>
 The array track is kept separate from the sequencing-based combined tracks
-(<a href="hgTrackUi?g=varFreqsAffected">Affected/Case Individuals</a> and
-<a href="hgTrackUi?g=varFreqsBackground">Population + Unaffected</a>) so that
+(<a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> and
+<a href="hgTrackUi?g=varFreqsBackground">Population reference</a>) so that
 sequencing-based and array-based frequencies can be inspected independently. For a summary
 of all available variant frequency databases, see the
 <a href="hgTrackUi?g=varFreqs">SNV Frequencies</a> supertrack page.
 </p>
 
 <h2>Display Conventions</h2>
 
 <h3>Color by Consequence</h3>
 <p>Variants are colored by their most severe predicted consequence:</p>
 <table class="stdTbl">
 <tr><th>Color</th><th>Consequence class</th><th>Examples</th></tr>
 <tr><th style="background-color:#FF0000;width:2em">&nbsp;</th>
     <td>Protein-truncating / loss-of-function</td>
     <td>stop_gained, frameshift, splice_donor, splice_acceptor, stop_lost, start_lost</td></tr>
 <tr><th style="background-color:#1F77B4;width:2em">&nbsp;</th>
@@ -47,31 +47,31 @@
 <h2>Caveats</h2>
 <p>
 Allele frequencies from genotyping arrays are not directly comparable to those from
 whole-genome or whole-exome sequencing. Two limitations to keep in mind:
 </p>
 <ul>
   <li><b>Probe coverage is sparse and curated.</b> Array variants are only those the
       manufacturer designed probes for. Absence from this track does <em>not</em> mean a
       variant is absent in that population, only that it was not on the chip.</li>
   <li><b>Per-variant call confidence varies and is sometimes unreported.</b> TPMI publishes
       a per-probe <code>NGS_concordance</code> value (chip-vs-sequencing concordance from
       its own validation) in the source VCF; high-AF claims with low concordance are
       common. MexBB ships only AN/AF/AC with no FILTER column and no per-site QC at all.
       For both arrays, high-AF rare-disease candidates should be cross-checked against the
       sequencing-based
-      <a href="hgTrackUi?g=varFreqsBackground">Population + Unaffected</a> track before
+      <a href="hgTrackUi?g=varFreqsBackground">Population reference</a> track before
       drawing conclusions.</li>
 </ul>
 
 <h2>Filters</h2>
 <p>
 This track supports filtering via the track settings page. Click the track title or use the
 &quot;Configure&quot; button to access filters.
 </p>
 
 <h3>Variant Type and Consequence</h3>
 <ul>
   <li><b>Variant Type</b>: SNV, Insertion, Deletion, or MNV.</li>
   <li><b>Consequence</b>: Missense, Synonymous, Stop Gained, Frameshift, Splice Donor,
       Splice Acceptor, Intron, 3' UTR, 5' UTR, Non-coding, Intergenic, or Other. The filter
       uses OR logic across the comma-separated consequence tokens on each variant. See the
@@ -93,32 +93,32 @@
 <p>
 The <b>Source Database</b> filter restricts the display to variants present in specific
 databases. It uses OR logic.
 </p>
 
 <h3>Length Filters</h3>
 <ul>
   <li><b>Reference/Alternate Length</b>: Filter by the length of the reference or alternate allele.</li>
   <li><b>Length Change</b>: Filter by the size difference between alternate and reference
       (positive = insertion, negative = deletion, zero = SNV or MNV).</li>
 </ul>
 
 <h2>Methods</h2>
 <p>
 The same merge-and-annotate pipeline used for the sequencing-based combined tracks
-(<a href="hgTrackUi?g=varFreqsAffected">Affected/Case Individuals</a> and
-<a href="hgTrackUi?g=varFreqsBackground">Population + Unaffected</a>) was run on the
+(<a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> and
+<a href="hgTrackUi?g=varFreqsBackground">Population reference</a>) was run on the
 array-cohort subset of source VCFs. Each VCF was stripped of its INFO fields, normalized
 with <code>bcftools norm</code> (splitting multi-allelic sites), and merged with
 <code>bcftools merge</code>. The merged VCF was then annotated with predicted protein
 consequences using <code>bcftools csq</code> with the
 <a href="https://www.ensembl.org/info/data/ftp/index.html" target="_blank">Ensembl</a>
 GRCh38 release 115 gene annotation (GFF3).
 </p>
 
 <p>
 The track's
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt"
 target="_blank">makeDoc file</a> documents how each source VCF was converted. Scripts are
 available from
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs"
 target="_blank">Github</a>.