diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java
index ae2c580a..e86da052 100644
--- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java
+++ b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java
@@ -226,7 +226,6 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVar
             Map<String, VariableVariantMasks> masks1 = variantMaskStorage1.get(key);
             Map<String, VariableVariantMasks> masks2 = variantMaskStorage2.get(key);
             if (masks2 == null) {
-                log.info("Key " + key + " not found in dataset 2");
                 masks2 = Map.of();
             }
 
@@ -247,12 +246,15 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVar
                     mergedMasks.put(entry.getKey(), new VariableVariantMasks(variantStore1.getPatientIds().length).append(entry.getValue()));
                 }
             }
-            merged.put(key, mergedMasks);
+            if (merged.keys().contains(key)) {
+                log.warn("Merged already contains key: " + key);
+            } else {
+                merged.put(key, mergedMasks);
+            }
         });
 
         variantMaskStorage2.keys().forEach(key -> {
             if (variantMaskStorage1.get(key) == null) {
-                log.info("Key " + key + " not found in dataset 1");
                 ConcurrentHashMap<String, VariableVariantMasks> mergedMasks = new ConcurrentHashMap<>();
                 Map<String, VariableVariantMasks> masks2 = variantMaskStorage2.get(key);
                 for (Map.Entry<String, VariableVariantMasks> entry : masks2.entrySet()) {
@@ -260,7 +262,11 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVar
                         mergedMasks.put(entry.getKey(), new VariableVariantMasks(variantStore1.getPatientIds().length).append(entry.getValue()));
                     }
                 }
-                merged.put(key, mergedMasks);
+                if (merged.keys().contains(key)) {
+                    log.warn("Second loop: merged already contains key: " + key);
+                } else {
+                    merged.put(key, mergedMasks);
+                }
             }
         });
         return merged;