86744c40b7e7f18792d287aedf9cf5da543e2d5a
max
  Fri Apr 17 07:22:27 2026 -0700
Add GA4K (Genomic Answers for Kids) small-variant subtrack to the
Variant Frequencies supertrack for hg38.
#Preview2 week - bugs introduced now will need a build patch to fix

Children's Mercy pediatric rare-disease cohort: ~36.2M SNVs and short
indels from 552 PacBio HiFi long-read samples (DeepVariant/GLnexus),
filtered to variants replicated in >=2 unrelated GA4K individuals or
an HPRC variant. Ref: Cohen et al. 2022, Genet Med, PMID 35305867.

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 7a69894d318..cecfeb0e22b 100644
--- src/hg/makeDb/trackDb/human/varFreqs.html
+++ src/hg/makeDb/trackDb/human/varFreqs.html
@@ -239,30 +239,39 @@
   <td>3.6k</td>
   <td>WGS</td>
   <td>Rare disease families (10.7k participants, 4.4k families)</td>
   <td>&mdash;</td>
   <td>No</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=hgdp1kFreq">gnomAD HGDP+1kG</a></td>
   <td>Global</td>
   <td>4k</td>
   <td>WGS</td>
   <td>80 populations (HGDP + 1000 Genomes reprocessed)</td>
   <td>80 populations, continental groups</td>
   <td>Yes</td>
 </tr>
+<tr>
+  <td><a href="hgTrackUi?g=ga4kSnv">GA4K</a></td>
+  <td>USA</td>
+  <td>552</td>
+  <td>PacBio HiFi long-read WGS</td>
+  <td>Genomic Answers for Kids: pediatric rare-disease probands and families (Children's Mercy)</td>
+  <td>&mdash;</td>
+  <td>Yes</td>
+</tr>
 </table>
 
 <h2>Display Conventions</h2>
 
 <p>Most tracks only show the variant and allele frequencies on mouseover or clicks.
 When zoomed in, tracks display alleles with base-specific coloring. Homozygote
 data are shown as one letter, while heterozygotes will be displayed with both
 letters. All VCF files are normalized, with one single allele per annotation (no multi-allele
 lines).
 </p>
 
 <h2>Data Access</h2>
 <p>All the data is publicly available. The table above indicates if we are allowed to distribute it in VCF format. Most of the databases do not allow us to redistribute the data files directly from our website, but it can always be downloaded from the original websites in some form. Click the database link in the table above and see the "Data Access" section of the respective track for a description of where to download the data. When the data is freely available from our website, the Data Access section will also indicate the VCF file location on our download server. Because it contains some licensed data, the combined track is not available for download, but can be recreated using the conversion scripts in our Github repository and the accompanying documentation file.
 </p>