diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
index 1b3e68647..5810bc94f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
@@ -181,15 +181,6 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
     @Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
     private double minIndelProportionToTriggerVariant = 0.05;
 
-    /**
-     * Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
-     * considered consensus.
-     */
-    @Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
-    private int nContigs = 2;
-
-
-
     /**
      * Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
      * A value of 0 turns downsampling off.
@@ -197,6 +188,14 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
     @Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
     private int downsampleCoverage = 250;
 
+    /**
+     * Number of chromossomes in the sample (this is used for the polyploid consensus compression). Only
+     * tested for humans (or organisms with n=2). Use at your own risk!
+     */
+    @Hidden
+    @Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
+    private int nContigs = 2;
+
     @Hidden
     @Argument(fullName = "", shortName = "dl", doc = "", required = false)
     private int debugLevel = 0;