Merging postreleasefix/113 to release/113

* postreleasefix/113: Update to version in tools data (#832) Add LOEUF plugin update in vep what's new (#831) Updated CADD version (#830)
Ensembl · Sep 18, 2024 · 54b1d5a · 54b1d5a
2 parents 40b02ee + eaab96c
commit 54b1d5a
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/docs/htdocs/info/docs/tools/vep/script/vep_download.html b/docs/htdocs/info/docs/tools/vep/script/vep_download.html
@@ -143,6 +143,10 @@ <h4>New in version [[SPECIESDEFS::ENSEMBL_VERSION]] <i>([[SPECIESDEFS::ENSEMBL_R
       <ul>
         <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/Paralogues.pm" rel="external">Paralogues</a></li>
       </ul>
+      <li>Plugin support added to REST for: </li>
+      <ul>
+        <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/LOEUF.pm" rel="external">LOEUF</a></li>
+      </ul>
       <li>Plugin data version updated for CADD (v1.6 to v1.7) and dbNSFP (4.5c to 4.7c).</li>
 
   </ul>

diff --git a/ensembl/htdocs/info/genome/variation/prediction/protein_function.html b/ensembl/htdocs/info/genome/variation/prediction/protein_function.html
@@ -97,7 +97,7 @@ <h2 id="CADD">CADD</h2>
       over 30 are predicted to be the 0.1% most deleterious possible substitutions in the human genome.<br />
       <b>We strongly recommend the actual score is used when assessing a variant and a cut-off appropriate to your requirements is chosen.</b>
     </p>
-    <p>CADD scores are taken from the <a rel="external" href="https://cadd.gs.washington.edu/download">CADD</a> project web site (version v1.6) for
+    <p>CADD scores are taken from the <a rel="external" href="https://cadd.gs.washington.edu/download">CADD</a> project web site (version v1.7) for
     consistency with other resources.</p>
   </div>
 </div>

diff --git a/tools_hive/conf/vep_plugins_hive_config.txt b/tools_hive/conf/vep_plugins_hive_config.txt
@@ -35,8 +35,8 @@
 
   CADD => {
     "params" => [
-      "snv=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_GRCh38_1.6_whole_genome_SNVs.tsv.gz",
-      "indels=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_GRCh38_1.6_InDels.tsv.gz",
+      "snv=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz",
+      "indels=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_GRCh38_1.7_InDels.tsv.gz",
       "snv_pig=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/ALL_pCADD-PHRED-scores.tsv.gz",
       "sv=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_prescored_variants.tsv.gz"
     ]