diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 7cc8e9e29..d37116215 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -469,7 +469,7 @@ public class GenomeAnalysisEngine {
                 throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName());
         }
         else {
-            final int SHARD_SIZE = walker instanceof RodWalker ? 100000000 : 100000;
+            final int SHARD_SIZE = walker instanceof RodWalker ? 1000000 : 100000;
             if(intervals == null)
                 return referenceDataSource.createShardsOverEntireReference(readsDataSource,genomeLocParser,SHARD_SIZE);
             else