diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantSourceEntry.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantSourceEntry.java
index f549d23d..276360ce 100644
--- a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantSourceEntry.java
+++ b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantSourceEntry.java
@@ -66,10 +66,7 @@ public AbstractVariantSourceEntry(String fileId, String studyId, String[] second
         this.fileId = fileId;
         this.studyId = studyId;
         if (secondaryAlternates != null) {
-            this.secondaryAlternates = Arrays.stream(secondaryAlternates)
-                    .map(a->a.toUpperCase())
-                    .collect(Collectors.toList())
-                    .toArray(new String[0]);
+            setSecondaryAlternates(secondaryAlternates);
         } else {
             this.secondaryAlternates = new String[]{};
         }
diff --git a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/filter/FilterBuilder.java b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/filter/FilterBuilder.java
index e3bb78c8..ed0e2c89 100644
--- a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/filter/FilterBuilder.java
+++ b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/filter/FilterBuilder.java
@@ -115,8 +115,8 @@ public FilterBuilder withVariantTypes(VariantType variantType) {
 
     public FilterBuilder withAlternates(List<String> alternates) {
         if (alternates != null && !alternates.isEmpty()) {
-            alternates = alternates.stream().map(a->a.toUpperCase()).collect(Collectors.toList());
-            filters.add(new VariantRepositoryAlternateFilter(alternates));
+            List<String> alternatesUppercase = alternates.stream().map(a->a.toUpperCase()).collect(Collectors.toList());
+            filters.add(new VariantRepositoryAlternateFilter(alternatesUppercase));
         }
         return this;
     }