a0f7abd772e0e0b47c4a64ffdc43527b39454ccf
gperez2
  Thu Dec 11 21:27:58 2025 -0800
Updating the data of the gnomAD v4.1 CNV track with the gnomad.v4.1.cnv.all.bed data, refs #36788

diff --git src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html
index 8738522aff9..44a994b5efc 100644
--- src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html
+++ src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html
@@ -2,35 +2,35 @@
 <p>
 The <b>${longLabel}</b> track set shows rare autosomal coding copy number variants (CNVs) with an overall
 site frequency of less than 1%. These variants were identified from exome sequencing (ES) data of
 464,297 individuals. The data can also be explored via the
 <a href="https://gnomad.broadinstitute.org/" target="_blank">gnomAD browser</a>.
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 Items are colored by the type of variant:
 <table class="stdTbl">
   <tr>
     <th>Variant Type</th>
   <tr>
     <td style="background-color: rgb(255,0,0)">Deletion (DEL)</td>
-    <td>20989</td>
+    <td>31939</td>
   </tr>
   <tr>
     <td style="background-color: rgb(0,0,255)">Duplication (DUP)</td>
-    <td>25026</td>
+    <td>36760</td>
   </tr>
 </table>.</p>
 
 <p><b>Mouseover</b> on an item will display the position, size of variant, genes impacted by
 variant (&gt;=10% CDS overlap by deletion or &gt;=75% CDS overlap by duplication), and site
 frequency of non-neuro control samples. Item description pages include a linkout to
 the gnomAD browser showing additional genetic ancestry group information.</p>
 
 
 <H2>Methods</H2>
 
 <h3>Exome CNV Discovery Method: GATK-gCNV</h3>
 <p>
 To identify rare coding CNVs from the ES data of 464,297 individuals in gnomAD v4, the GATK-gCNV
 method was employed, as described in Babadi et al., Nat Genet, 2023.</p>
@@ -65,31 +65,31 @@
       dataset.</li>
   <li>This dataset only includes variants that span three or more exons that received sufficient
       coverage.</li>
   <li>This dataset is limited to autosomal CNVs for now.</li>
 </ol>
 
 <p>
 More information can be found at the
 <a href="https://gnomad.broadinstitute.org/news/2023-11-v4-copy-number-variants/" target="_blank">
 gnomAD site</a>.</p>
 
 <p>
 The bed files was obtained from the gnomAD Google Storage bucket:</p>
 
 <pre>
-https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/exome_cnv/gnomad.v4.1.cnv.non_neuro_controls.bed
+https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/exome_cnv/gnomad.v4.1.cnv.all.bed
 </pre>
 
 The data was then transformed into a bigBed track. For the full list of commands used to make this
 track please see the &quot;gnomAD CNVs v4.1&quot; section of the
 <a href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg38/gnomad.txt"
 target="_blank">makedoc</a>.</p>
 
 
 <h2>Data Access</h2>
 <p>
 The raw data can be explored interactively with the <a href="../hgTables">Table Browser</a>, or
 the <a href="../hgIntegrator">Data Integrator</a>. For automated access, this track, like all 
 others, is available via our <a href="../goldenPath/help/api.html">API</a>.  However, for bulk 
 processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed 
 file that can be downloaded from the