diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 4a814b1a0..bda9babf8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Window;
+import org.broadinstitute.sting.gatk.walkers.Hidden;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
@@ -112,12 +113,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     // DEBUGGING OPTIONS FOLLOW
 
+    @Hidden
     @Argument(fullName="indelsFileForDebugging", shortName="indels", required=false, doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY")
     protected String OUT_INDELS = null;
 
+    @Hidden
     @Argument(fullName="statisticsFileForDebugging", shortName="stats", doc="print out statistics (what does or doesn't get cleaned); FOR DEBUGGING PURPOSES ONLY", required=false)
     protected String OUT_STATS = null;
 
+    @Hidden
     @Argument(fullName="SNPsFileForDebugging", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out; FOR DEBUGGING PURPOSES ONLY", required=false)
     protected String OUT_SNPS = null;