diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 0c63eb752..1173f6cef 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -29,16 +29,16 @@ import java.util.regex.Pattern;
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
 public class SelectVariants extends RodWalker<Integer, Integer> {
-    @Argument(fullName="sample", shortName="SN", doc="Sample(s) to include.  Can be a single sample, specified multiple times for many samples, or a regular expression to select many samples.", required=false)
+    @Argument(fullName="sample", shortName="sn", doc="Sample(s) to include.  Can be a single sample, specified multiple times for many samples, or a regular expression to select many samples.", required=false)
     public Set<String> SAMPLE_EXPRESSIONS;
 
     @Argument(shortName="select", doc="One or more criteria to use when selecting the data.  Evaluated *after* the specified samples are extracted and the INFO-field annotations are updated.", required=false)
     public ArrayList<String> SELECT_EXPRESSIONS = new ArrayList<String>();
 
-    @Argument(fullName="excludeNonVariants", shortName="ENV", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
+    @Argument(fullName="excludeNonVariants", shortName="env", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
     private boolean EXCLUDE_NON_VARIANTS = false;
 
-    @Argument(fullName="excludeFiltered", shortName="EF", doc="Don't include filtered loci.", required=false)
+    @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci.", required=false)
     private boolean EXCLUDE_FILTERED = false;
 
     private ArrayList<String> selectNames = new ArrayList<String>();