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/varFreqsBackground.html src/hg/makeDb/trackDb/human/varFreqsBackground.html
index e63ca161efb..4a7f3b9f2b2 100644
--- src/hg/makeDb/trackDb/human/varFreqsBackground.html
+++ src/hg/makeDb/trackDb/human/varFreqsBackground.html
@@ -1,35 +1,35 @@
 <h2>Description</h2>
 <p>
 This track shows small variants (SNVs and short indels) seen in <b>population reference
 cohorts and in unaffected or control individuals</b> of disease-study cohorts, annotated
 with their predicted protein consequence and colored by severity. It is the background half
 of a matched pair: the companion
-<a href="hgTrackUi?g=varFreqsAffected">Affected/Case Individuals</a> track shows the same
+<a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> track shows the same
 kind of variants seen in affected or case individuals. Displaying the two together lets you
 see how common a variant is in the general/unaffected population compared with affected
 individuals. For the full list of contributing projects, see the
 <a href="hgTrackUi?g=varFreqs">SNV Frequencies</a> collection page.
 </p>
 <p>
 The background combines two kinds of data: the population/biobank reference cohorts (such as
 gnomAD HGDP+1kG, TOPMed, ALFA, HRC and the many national WGS projects), and the
 unaffected/control or unknown-phenotype arms of the disease-study cohorts (non-ASD family
 members in SFARI SPARK WES/WGS, SCHEMA controls, and GREGoR unaffected/unknown
 participants). Genotyping-array cohorts are not included. A variant that also appears in
 affected individuals is shown in both this track and the
-<a href="hgTrackUi?g=varFreqsAffected">Affected/Case Individuals</a> track.
+<a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> track.
 </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>
     <td>Missense / in-frame</td>
     <td>missense, inframe_insertion, inframe_deletion, protein_altering</td></tr>
 <tr><th style="background-color:#008000;width:2em">&nbsp;</th>
     <td>Synonymous</td>
@@ -77,34 +77,34 @@
   <li><b>Reference/Alternate Length</b> and <b>Length Change</b>: filter by allele length.</li>
 </ul>
 
 <h2>Methods</h2>
 <p>
 Variant-frequency VCFs from the contributing cohorts were stripped of unneeded INFO fields,
 normalized with <code>bcftools norm</code> (splitting multi-allelic sites), and merged with
 <code>bcftools merge</code>. The merged callset was annotated with predicted protein
 consequences using <a href="https://samtools.github.io/bcftools/howtos/csq-calling.html"
 target="_blank">bcftools csq</a> against the
 <a href="https://www.ensembl.org/info/data/ftp/index.html" target="_blank">Ensembl</a>
 GRCh38 release 115 gene models.
 </p>
 <p>
 A custom Python script (<code>vcfToBigBed.py</code>) then read the per-cohort allele
-frequencies and, for each variant, summed/maximized the counts across the population cohorts
-and unaffected/control subgroups to produce this track, and across the affected arms to
-produce the companion
-<a href="hgTrackUi?g=varFreqsAffected">Affected/Case Individuals</a> track. A variant seen
+counts and frequencies and, for each variant, pooled the allele counts and allele numbers
+across the population cohorts and unaffected/control subgroups to produce this track, and
+across the affected arms to produce the companion
+<a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> track. A variant seen
 in both groups appears in both tracks. The build is documented in the
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt"
 target="_blank">makeDoc</a>, and the scripts are on
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs"
 target="_blank">GitHub</a>.
 </p>
 
 <h2>Data Access</h2>
 <p>
 Because the merged callset combines cohorts whose redistribution licenses differ, this
 track is <b>not available for download</b> and is not in the Table Browser. It can be
 reconstructed from the individual source VCFs using the
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs"
 target="_blank">conversion scripts</a> and the
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt"