9a49afb16653363a70d8e4d205513008b7b08df5
max
  Wed May 13 06:18:42 2026 -0700
varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html
index dbdb68feb5e..0f2e88374dd 100644
--- src/hg/makeDb/trackDb/human/varFreqs.html
+++ src/hg/makeDb/trackDb/human/varFreqs.html
@@ -10,32 +10,31 @@
 with filters, summed population frequencies and recalculated protein-effect annotations.
 In addition, there is one subtrack per project with the original VCF data and all the annotations that the project provides.
 The different projects use different pipelines and sequencing technologies, click any of the projects 
 above or below for a summary of their sample selection, sequencing assay and software pipeline.
 Many projects do not allow us to distribute the data but we document how the
 data can be requested and provide all converters.</p>
 
 <p>
 Data from projects that provide haplotype-phased genotypes can also be found
 elsewhere: 1000 Genomes is also a separate track, and the phased genotypes HGDP, SGDP,
 HGDP+1000 Genomes and Mexico Biobank can also be found in the &quot;Phased Variants&quot; track.
 Their VCF versions below show only the isolate frequency per variant.
 </p>
 
 <p>Please contact us (<A HREF="mailto:&#103;en&#111;&#109;&#101;&#64;&#115;&#111;&#101;.&#117;&#99;s&#99;.&#101;&#100;u">&#103;en&#111;&#109;&#101;&#64;&#115;&#111;&#101;.&#117;&#99;s&#99;.&#101;&#100;u</A><!-- above address is genome at soe.ucsc.edu -->), if you know a project that we should add. So far,
-we already requested these: UK Biobank (pending for a year),
-Regeneron&apos;s Million Exomes and Mexico City Studies (request rejected), Taiwan Biobank (pending).
+Regeneron&apos;s Million Exomes and Mexico City Studies (request rejected) and Taiwan Biobank (pending).
 </p>
 
 <h2>Combined Track (All Databases)</h2>
 <p>
 The &quot;All Databases Combined&quot; track merges variants from all individual databases into a single
 bigBed file with consequence annotations, totaling 1.17 billion variants from ~1.7 million individuals.
 The track supports filtering by variant type
 (SNV, insertion, deletion, MNV), predicted consequence (missense, synonymous, stop gained,
 frameshift, splice, intron, intergenic), source database, allele frequency (overall maximum
 and per-database), and allele count (total or per-database). This track is either useful in dense mode
 for getting a quick overview of variant density across all projects, or with filters to find
 variants present in specific databases or within certain frequency ranges. Note that with the &quot;clone track&quot;
 feature you can clone this track and have multiple versions, each with different filters activated.
 You can also use our &quot;Density mode&quot; checkbox on the track configuration page to show a plot with the
 density of variants passing a filter, one per track clone.
@@ -105,30 +104,39 @@
   <td>408k</td>
   <td>WGS/WES/array mix</td>
   <td>Aggregated dbGaP studies, mixed phenotypes</td>
   <td>&mdash;</td>
   <td>Yes</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=finngen">FinnGen R12</a></td>
   <td>Finland</td>
   <td>500k</td>
   <td>Imputed (8.5k WGS ref panel)</td>
   <td>National biobank, ~10% of population</td>
   <td>&mdash;</td>
   <td>Yes</td>
 </tr>
+<tr>
+  <td><a href="hgTrackUi?g=ukbb">UK Biobank (Neale Lab v3)</a></td>
+  <td>UK</td>
+  <td>361k</td>
+  <td>Imputed array (HRC+UK10K+1KGp3 ref panel)</td>
+  <td>White British subset of UK Biobank, Neale Lab Round 2 GWAS</td>
+  <td>&mdash;</td>
+  <td>Yes</td>
+</tr>
 <tr>
   <td><a href="hgTrackUi?g=swefreq">SweGen</a></td>
   <td>Sweden</td>
   <td>1k</td>
   <td>WGS</td>
   <td>Cross-section of Swedish population</td>
   <td>&mdash;</td>
   <td>No</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=schema">SCHEMA</a></td>
   <td>Multi-national</td>
   <td>121k</td>
   <td>WES</td>
   <td>Schizophrenia: 24k cases, 97k controls</td>