diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index ebeb159f0..38cb18d20 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -271,12 +271,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             }
             sb.setCharAt(sb.length()-2, ']');
             sb.setCharAt(sb.length()-1, ' ');
-            sb.append("pQ=");
-            sb.append(PRESERVE_QSCORES_LESS_THAN);
-            sb.append(" maxQ=");
-            sb.append(MAX_QUALITY_SCORE);
-            sb.append(" smoothing=");
-            sb.append(SMOOTHING);
             programRecord.setCommandLine(sb.toString());
 
             List<SAMProgramRecord> oldRecords = header.getProgramRecords();