diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf
index a23204b2..fdc641ad 100644
--- a/modules/nf-core/vcf2db/main.nf
+++ b/modules/nf-core/vcf2db/main.nf
@@ -29,6 +29,12 @@ process VCF2DB {
         ${prefix}.db \\
         $args
 
+    sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)'
+    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)'
+    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)'
+    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)'
+    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)'
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         vcf2db: $VERSION
diff --git a/modules/nf-core/vcf2db/vcf2db.diff b/modules/nf-core/vcf2db/vcf2db.diff
index 45757135..524bb0db 100644
--- a/modules/nf-core/vcf2db/vcf2db.diff
+++ b/modules/nf-core/vcf2db/vcf2db.diff
@@ -12,6 +12,19 @@ Changes in 'vcf2db/main.nf':
  
      // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
      conda "${moduleDir}/environment.yml"
+@@ -29,6 +29,12 @@
+         ${prefix}.db \\
+         $args
+ 
++    sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)'
++    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)'
++    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)'
++    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)'
++    sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)'
++
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+         vcf2db: $VERSION
 
 'modules/nf-core/vcf2db/tests/main.nf.test.snap' is unchanged
 'modules/nf-core/vcf2db/tests/tags.yml' is unchanged