diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
index 2969888b2..f24136cd3 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
@@ -72,7 +72,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     private String PLATFORM = "SLX";
     @Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
     private int WINDOW_SIZE = 3;
-    @Argument(fullName="recal_file", shortName="rf", required=false, doc="Filename for the outputted covariates table recalibration file")
+    @Argument(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the outputted covariates table recalibration file")
     private String RECAL_FILE = "output.recal_data.csv";
     @Argument(fullName="noPrintHeader", shortName="noHeader", required=false, doc="Don't print the usual header on the table recalibration file")
     private boolean NO_PRINT_HEADER = false;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
index 1190430b9..9f519cb2e 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
@@ -56,7 +56,7 @@ import java.io.FileNotFoundException;
 @WalkerName("TableRecalibrationRefactored")
 public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
 
-    @Argument(fullName="recal_file", shortName="rf", doc="Input recalibration table file generated by CountCovariates", required=true)
+    @Argument(fullName="recal_file", shortName="recalFile", doc="Input recalibration table file generated by CountCovariates", required=true)
     public String RECAL_FILE;
     @Argument(fullName="outputBam", shortName="outputBam", doc="output BAM file", required=false)
     public SAMFileWriter OUTPUT_BAM = null;