diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index fee6dfd7e..294d06615 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -387,7 +387,7 @@ public class GenomeAnalysisEngine {
         if(readsDataSource != null && !readsDataSource.hasIndex() ) { 
             if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
                 throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed.  The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.");
-            if(intervals != null)
+            if(intervals != null && !argCollection.allowIntervalsWithUnindexedBAM)
                 throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available.");
 
             Shard.ShardType shardType;
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index d976c1efe..4d00262d3 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -237,6 +237,11 @@ public class GATKArgumentCollection {
     @Hidden
     public int processTrackerID = -1;
 
+    @Element(required = false)
+    @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM.  NO INTEGRATION TESTS are available.  Use at your own risk.")
+    @Hidden
+    public boolean allowIntervalsWithUnindexedBAM = false;
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // methods
@@ -420,6 +425,9 @@ public class GATKArgumentCollection {
         if ( processTrackerID != other.processTrackerID )
             return false;
 
+        if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM)
+            return false;
+
         return true;
     }