diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 228f8351a..967fd3236 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -797,6 +797,15 @@ public class GenomeAnalysisEngine {
         if ( getWalkerBAQApplicationTime() == BAQ.ApplicationTime.FORBIDDEN && argCollection.BAQMode != BAQ.CalculationMode.OFF)
             throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + argCollection.BAQMode + " was requested.");
 
+        if (argCollection.removeProgramRecords && argCollection.keepProgramRecords)
+            throw new UserException.BadArgumentValue("rpr / kpr", "Cannot enable both options");
+
+        // LocusWalkers don't use program records, so remove them by default to save memory
+        boolean removeProgramRecords = (this.walker instanceof LocusWalker) || argCollection.removeProgramRecords;
+
+        if (argCollection.keepProgramRecords)
+            removeProgramRecords = false;
+
         return new SAMDataSource(
                 samReaderIDs,
                 threadAllocation,
@@ -814,7 +823,7 @@ public class GenomeAnalysisEngine {
                 refReader,
                 getBaseRecalibration(),
                 argCollection.defaultBaseQualities,
-                argCollection.removeProgramRecords);
+                removeProgramRecords);
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 91a008cbc..972116952 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -249,9 +249,12 @@ public class GATKArgumentCollection {
     @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
     public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
 
-    @Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Should we remove program records from the SAM header", required = false)
+    @Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Should we override the Walker's default and remove program records from the SAM header", required = false)
     public boolean removeProgramRecords = false;
 
+    @Argument(fullName = "keep_program_records", shortName = "kpr", doc = "Should we override the Walker's default and keep program records from the SAM header", required = false)
+    public boolean keepProgramRecords = false;
+
     @Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations: nothing will be checked at runtime.  For expert users only who know what they are doing.  We do not support usage of this argument.", required = false)
     public ValidationExclusion.TYPE unsafe;