37a5b97198453bd06cb03d2092cae239f368e84c
max
  Wed Apr 29 05:49:14 2026 -0700
varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift)

Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each
from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana),
sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff
lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not
permitted, so tableBrowser is disabled.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642

diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html
index 0e9f236cd67..79c3488323b 100644
--- src/hg/makeDb/trackDb/human/varFreqs.html
+++ src/hg/makeDb/trackDb/human/varFreqs.html
@@ -266,30 +266,39 @@
   <td>1,027</td>
   <td>PacBio HiFi long-read WGS</td>
   <td>Consortium of Long Read Sequencing: aggregated population-consented samples across multiple research cohorts</td>
   <td>&mdash;</td>
   <td>Yes</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=svatalogSnv">SVatalog 101</a></td>
   <td>Canada (SickKids)</td>
   <td>101</td>
   <td>10X Genomics linked short-read WGS</td>
   <td>GWAS SVatalog cohort: 101 samples with matched long-read SVs (see <a href="hgTrackUi?g=chirmade101Sv">chirmade101Sv</a>)</td>
   <td>&mdash;</td>
   <td>Yes</td>
 </tr>
+<tr>
+  <td><a href="hgTrackUi?g=tishkoff180">Indigenous Africans 180</a></td>
+  <td>Africa (Ethiopia, Tanzania, Cameroon, Botswana)</td>
+  <td>180</td>
+  <td>WGS (&gt;30x)</td>
+  <td>12 indigenous populations across all four African language phyla (Khoesan, Niger-Congo, Nilo-Saharan, Afroasiatic)</td>
+  <td>&mdash;</td>
+  <td>No</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>