diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
index 6b18fa4e2..362431efb 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
@@ -29,7 +29,7 @@ import java.util.List;
  *
  */
 public class MicroManager {
-    private static long SHARD_SIZE = 5L;
+    private static long SHARD_SIZE = 100000L;
 
     private File reads;
     private FastaSequenceFile2 ref;
@@ -86,6 +86,10 @@ public class MicroManager {
                         fl.add(new File(line));
                     }
                 }
+            } else if (reads.getCanonicalPath().indexOf(",") > 0) {
+                for (String bamFile : reads.getCanonicalPath().split(",")) {
+                    fl.add(new File(bamFile));
+                }
 
             } else {
                 fl.add(reads);