diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index 2ea4bdfb0..00c6ddae8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -123,13 +123,13 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
 
         // This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
         // therefore, the user must have failed to specify a type default
-        if(writerFileName.asFile() == null && generateMD5)
+        if(writerFileName != null && writerFileName.asFile() == null && generateMD5)
                 throw new ArgumentException("MD5 generation specified, but no output file specified.  If md5 generation is desired, please specify a BAM output file and an md5 file will be written alongside.");
 
         // Create the stub and set parameters.
         SAMFileWriterStub stub = null;      // stub = new SAMFileWriterStub(engine, defaultOutputStream);
 
-        if ( writerFileName.asFile() != null ) {
+        if (writerFileName != null &&  writerFileName.asFile() != null ) {
             stub = new SAMFileWriterStub(engine, writerFileName.asFile());
 
             if ( compressionLevel != null )