diff --git a/nextflow/vcf_prepper/bin/generate_vep_config.py b/nextflow/vcf_prepper/bin/generate_vep_config.py
index b1e9e737..fc93bf56 100755
--- a/nextflow/vcf_prepper/bin/generate_vep_config.py
+++ b/nextflow/vcf_prepper/bin/generate_vep_config.py
@@ -70,6 +70,9 @@
     "Downstream",
     "ClinPred",
 ]
+SV_PLUGINS = [
+    "CADD"
+]
 
 
 def parse_args(args=None):
@@ -293,6 +296,7 @@ def get_plugin_args(
     species: str,
     assembly: str,
     conservation_data_dir: str = CONSERVATION_DATA_DIR,
+    structural_variant: bool = False
 ) -> str:
     """Return plugin configuration line(s) for the requested plugin.
 
@@ -305,6 +309,7 @@ def get_plugin_args(
         species (str): Species production name.
         assembly (str): Assembly name.
         conservation_data_dir (str): Directory containing conservation plugin data.
+        structural_variant (str): Structural variant or not.
 
     Returns:
         str|None: Plugin argument string for inclusion in VEP config, or None to skip plugin.
@@ -318,20 +323,25 @@ def get_plugin_args(
         if version < 113:
             plugin_data_dir = plugin_data_dir.replace(f"{version}", "113")
 
-        if species == "sus_scrofa":
-            snv = os.path.join(plugin_data_dir, f"ALL_pCADD-PHRED-scores.tsv.gz")
-            check_plugin_files(plugin, [snv])
+        if structural_variant:
+            sv = os.path.join(plugin_data_dir, f"CADD_prescored_variants.tsv.gz")
+            check_plugin_files(plugin, [sv])
 
-            return f"CADD,{snv}"
+            return f"CADD,{sv}"
+        else:
+            if species == "sus_scrofa":
+                snv = os.path.join(plugin_data_dir, f"ALL_pCADD-PHRED-scores.tsv.gz")
+                check_plugin_files(plugin, [snv])
 
-        snv = os.path.join(
-            plugin_data_dir, f"CADD_{assembly}_1.7_whole_genome_SNVs.tsv.gz"
-        )
-        indels = os.path.join(plugin_data_dir, f"CADD_{assembly}_1.7_InDels.tsv.gz")
-
-        check_plugin_files(plugin, [snv, indels])
+                return f"CADD,{snv}"
+            else:
+                snv = os.path.join(
+                    plugin_data_dir, f"CADD_{assembly}_1.7_whole_genome_SNVs.tsv.gz"
+                )
+                indels = os.path.join(plugin_data_dir, f"CADD_{assembly}_1.7_InDels.tsv.gz")
+                check_plugin_files(plugin, [snv, indels])
 
-        return f"CADD,{snv},{indels}"
+                return f"CADD,{snv},{indels}"
 
     if plugin == "REVEL":
         data_file = f"/nfs/production/flicek/ensembl/variation/data/REVEL/2021-may/new_tabbed_revel_{assembly.lower()}.tsv.gz"
@@ -492,6 +502,7 @@ def get_plugins(
     assembly: str,
     repo_dir: str = REPO_DIR,
     conservation_data_dir: str = CONSERVATION_DATA_DIR,
+    structural_variant: bool = False
 ) -> list:
     """Assemble plugin argument strings for the species and version.
 
@@ -501,17 +512,21 @@ def get_plugins(
         assembly (str): Assembly name.
         repo_dir (str): Repository directory.
         conservation_data_dir (str): Conservation plugin data directory.
+        structural_variant (str): Structural variant or not.
 
     Returns:
         list: List of plugin argument strings to include in the VEP config.
     """
+    plugin_list = PLUGINS
+    if structural_variant:
+        plugin_list = SV_PLUGINS
     plugins = []
 
-    for plugin in PLUGINS:
+    for plugin in plugin_list:
         plugin_species = get_plugin_species(plugin, repo_dir)
         if len(plugin_species) == 0 or species in plugin_species:
             plugin_args = get_plugin_args(
-                plugin, version, species, assembly, conservation_data_dir
+                plugin, version, species, assembly, conservation_data_dir, structural_variant
             )
             if plugin_args is not None:
                 plugins.append(plugin_args)
@@ -619,7 +634,7 @@ def main(args=None):
     else:
         print(f"[WARNING] Invalid population config file - {population_data_file}")
 
-    plugins = get_plugins(species, version, assembly, repo_dir, conservation_data_dir)
+    plugins = get_plugins(species, version, assembly, repo_dir, conservation_data_dir, structural_variant)
 
     # write the VEP config file
     with open(vep_config, "w") as file: