diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 3be87da80..722326018 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -132,6 +132,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
     protected List<String> annotationsToUse = new ArrayList<String>();
 
+    /**
+     * Note that this argument has higher priority than the -A or -G arguments,
+     * so annotations will be excluded even if they are explicitly included with the other options.
+     */
+    @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
+    protected List<String> annotationsToExclude = new ArrayList<String>();
+
     /**
      * See the -list argument to view available groups.
      */
@@ -148,6 +155,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     @Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls; see documentation for more details", required=false)
     protected List<String> expressionsToUse = new ArrayList<String>();
 
+    /**
+     * Note that the -XL argument can be used along with this one to exclude annotations.
+     */
     @Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
     protected Boolean USE_ALL_ANNOTATIONS = false;
 
@@ -209,9 +219,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         }
 
         if ( USE_ALL_ANNOTATIONS )
-            engine = new VariantAnnotatorEngine(this, getToolkit());
+            engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
         else
-            engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, this, getToolkit());
+            engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
         engine.initializeExpressions(expressionsToUse);
 
         // setup the header fields
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index e5effe6d8..e4bc0d5d5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -73,19 +73,20 @@ public class VariantAnnotatorEngine {
     }
 
     // use this constructor if you want all possible annotations
-    public VariantAnnotatorEngine(AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
+    public VariantAnnotatorEngine(List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
         this.walker = walker;
         this.toolkit = toolkit;
         requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
         requestedGenotypeAnnotations = AnnotationInterfaceManager.createAllGenotypeAnnotations();
+        excludeAnnotations(annotationsToExclude);
         initializeDBs();
     }
 
     // use this constructor if you want to select specific annotations (and/or interfaces)
-    public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
+    public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
         this.walker = walker;
         this.toolkit = toolkit;
-        initializeAnnotations(annotationGroupsToUse, annotationsToUse);
+        initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude);
         initializeDBs();
     }
 
@@ -96,10 +97,30 @@ public class VariantAnnotatorEngine {
             requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
     }
 
-    private void initializeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse) {
+    private void initializeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude) {
         AnnotationInterfaceManager.validateAnnotations(annotationGroupsToUse, annotationsToUse);
         requestedInfoAnnotations = AnnotationInterfaceManager.createInfoFieldAnnotations(annotationGroupsToUse, annotationsToUse);
         requestedGenotypeAnnotations = AnnotationInterfaceManager.createGenotypeAnnotations(annotationGroupsToUse, annotationsToUse);
+        excludeAnnotations(annotationsToExclude);
+    }
+
+    private void excludeAnnotations(List<String> annotationsToExclude) {
+        if ( annotationsToExclude.size() == 0 )
+            return;
+
+        List<InfoFieldAnnotation> tempRequestedInfoAnnotations = new ArrayList<InfoFieldAnnotation>(requestedInfoAnnotations.size());
+        for ( InfoFieldAnnotation annotation : requestedInfoAnnotations ) {
+            if ( !annotationsToExclude.contains(annotation.getClass().getSimpleName()) )
+                tempRequestedInfoAnnotations.add(annotation);
+        }
+        requestedInfoAnnotations = tempRequestedInfoAnnotations;
+
+        List<GenotypeAnnotation> tempRequestedGenotypeAnnotations = new ArrayList<GenotypeAnnotation>(requestedGenotypeAnnotations.size());
+        for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
+            if ( !annotationsToExclude.contains(annotation.getClass().getSimpleName()) )
+                tempRequestedGenotypeAnnotations.add(annotation);
+        }
+        requestedGenotypeAnnotations = tempRequestedGenotypeAnnotations;
     }
 
     private void initializeDBs() {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 9fdf65015..72dc217e1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -149,6 +149,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
     protected List<String> annotationsToUse = new ArrayList<String>();
 
+    /**
+     * Which annotations to exclude from output in the VCF file.  Note that this argument has higher priority than the -A or -G arguments,
+     * so annotations will be excluded even if they are explicitly included with the other options.
+     */
+    @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
+    protected List<String> annotationsToExclude = new ArrayList<String>();
+
     /**
      * Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
      */
@@ -210,7 +217,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         if ( verboseWriter != null )
             verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tAFposterior\tNormalizedPosterior");
 
-        annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, this, getToolkit());
+        annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
 
         // initialize the header
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 04bff8d41..2fed668c5 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("8e7de435105499cd71ffc099e268a83e"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
@@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("64b6804cb1e27826e3a47089349be581"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
@@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
@@ -71,15 +71,23 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("09f8e840770a9411ff77508e0ed0837f"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
+    @Test
+    public void testExcludeAnnotations() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("b49fe03aa4b675db80a9db38a3552c95"));
+        executeTest("test exclude annotations", spec);
+    }
+
     @Test
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                baseTestString() + " -G Standard --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
                 Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
         executeTest("test overwriting header", spec);
     }
@@ -87,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
         executeTest("not passing it any reads", spec);
     }
@@ -103,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
         executeTest("getting DB tag with HM3", spec);
     }
@@ -111,7 +119,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
+                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
                 Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
         executeTest("using expression", spec);
     }
@@ -121,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
-                    baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
+                    baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + file + " -BTI variant -NO_HEADER", 1,
                     Arrays.asList(MD5));
             executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
         }