diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
index c34b942b148..73a256a794c 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
@@ -528,7 +528,7 @@ else if ( funcotatorArgs.referenceVersion.equals(BaseFuncotatorArgumentCollectio
         }
 
         // Record whether we need to revert the contigs back to B37 after annotation:
-        if (FuncotatorUtils.isSequenceDictionaryUsingB37Reference(sequenceDictionaryForDrivingVariants) && mustConvertInputContigsToHg19) {
+        if (mustConvertInputContigsToHg19 && FuncotatorUtils.isSequenceDictionaryUsingB37Reference(sequenceDictionaryForDrivingVariants)) {
             this.mustRevertVariantContigsFromHg19ToB37 = true;
         }