diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 1f214fa62..a509fec0f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -35,6 +35,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.util.List;
+
 
 /**
  * Generates an alternative reference sequence over the specified interval.  Given variant ROD tracks,
@@ -45,6 +47,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 @Reference(window=@Window(start=-1,stop=50))
 @Requires(value={DataSource.REFERENCE})
 public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
+
+    @Input(fullName = "variants", shortName = "V", doc="variants to model", required=false)
+    public List<RodBinding<VariantContext>> variants;
+
     @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
     public RodBinding<VariantContext> snpmask = RodBinding.makeUnbound(VariantContext.class);
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
index be2f3cdaa..9af39e92c 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
@@ -24,16 +24,15 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         executeTest("testFastaReference", spec1b);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
                  1,
                  Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
-        // TODO : Eric, update with new DBSNP
-//        WalkerTestSpec spec3 = new WalkerTestSpec(
-//                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:snps,GeliText " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B:snpmask,dbsnp " + GATKDataLocation + "dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
-//                 1,
-//                 Arrays.asList("82705a88f6fc25880dd2331183531d9a"));
-//        executeTest("testFastaAlternateReferenceSnps", spec3);
+        WalkerTestSpec spec3 = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + GATKDataLocation + "dbsnp_129_b36.vcf -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
+                 1,
+                 Arrays.asList("8b6cd2e20c381f9819aab2d270f5e641"));
+        executeTest("testFastaAlternateReferenceSnps", spec3);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
index 4405f61d7..86f8b14f1 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
@@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
-                        " -dbsnp,VCF " + b36dbSNP129 +
+                        " -dbsnp:VCF " + b36dbSNP129 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
@@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
-                        " -dbsnp,vcf " + b36dbSNP129 +
+                        " -dbsnp:vcf " + b36dbSNP129 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
@@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -L chr1:1-50,000,000" +
                         " -nt 10" +
-                        " -dbsnp,vcf " + b36dbSNP129 +
+                        " -dbsnp:vcf " + b36dbSNP129 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
index e8b5033cf..200b9b5a7 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
@@ -30,7 +30,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                         " -LOD 5" +
                         " -maxConsensuses 100" +
                         " -greedy 100" +
-                        " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -dbsnp:vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -o /dev/null" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-5,650,000" +
@@ -45,7 +45,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                         " -LOD 5" +
                         " -maxConsensuses 100" +
                         " -greedy 100" +
-                        " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -dbsnp:vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -o /dev/null" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L chr1:1-150,000,000" +
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
index f65ba2cf0..df247aed5 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
@@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " --variant:dbsnp " + GATKDataLocation + "dbsnp_129_b36.rod" +
+                        " --variant:dbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" +
                         " -T VariantsToVCF" +
                         " -L 1:1-30,000,000" +
                         " -o %s" +