diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java
index d70b2df829e..ddbbaf1ac4d 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java
@@ -137,7 +137,7 @@ public class FilterAlignmentArtifacts extends MultiVariantWalkerGroupedOnStart {
 
     @Advanced
     @Argument(fullName = AssemblyBasedCallerArgumentCollection.SMITH_WATERMAN_LONG_NAME, doc = "Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice", optional = true)
-    public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.JAVA;
+    public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.FASTEST_AVAILABLE;
 
 
     @ArgumentCollection