diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
new file mode 100644
index 000000000..b77b175bc
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.arguments;
+
+
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.simpleframework.xml.*;
+
+/**
+ * @author ebanks
+ * @version 1.0
+ */
+@Root
+public class DbsnpArgumentCollection {
+
+    /**
+      * A dbSNP VCF file.
+      */
+    @Input(fullName="dbsnp", shortName = "D", doc="dbSNP file", required=false)
+    public RodBinding<VariantContext> dbsnp = RodBinding.makeUnbound(VariantContext.class);
+
+}
+
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 ec7d51043..594216d53 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -34,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
@@ -60,6 +62,23 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
     public RodBinding<SnpEffFeature> snpEffFile;
 
+    /**
+      * A dbSNP VCF file from which to annotate.
+      *
+      * rsIDs from this file are used to populate the ID column of the output.  Also, the DB INFO flag will be set when appropriate.
+      */
+    @ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
+
+    /**
+      * A comparisons VCF file from which to annotate.
+      *
+      * If a record in the 'variant' track overlaps with a record from the provided comp track, the INFO field will be annotated
+      *  as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field).  Records that are filtered in the comp track will be ignored.
+      *  Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
+      */
+    @Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
+    public RodBinding<VariantContext> comps = RodBinding.makeUnbound(VariantContext.class);
+
     @Output(doc="File to which variants should be written",required=true)
     protected VCFWriter vcfWriter = null;
 
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 812511322..6836b14fc 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
@@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
@@ -59,6 +60,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
 
     @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
 
+    /**
+      * A dbSNP VCF file from which to annotate.
+      *
+      * rsIDs from this file are used to populate the ID column of the output.  Also, the DB INFO flag will be set when appropriate.
+      */
+    @ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
+
     // control the output
     @Output(doc="File to which variants should be written",required=true)
     protected VCFWriter writer = null;