diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 0ccfeb40b..d77ed666a 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -753,6 +753,10 @@ public class GenomeAnalysisEngine {
         if (reads.getReadsFiles().size() == 0)
             return null;
 
+        // Force dynamic merging to use original sharding method until memory usage is under control.
+        if (reads.getReadsFiles().size() > 1)
+            argCollection.disableExperimentalSharding = true;
+
         SAMDataSource dataSource = null;
         if(!argCollection.disableExperimentalSharding)
             dataSource = new BlockDrivenSAMDataSource(reads);