diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
index 80c971601..6ae34f190 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
@@ -45,32 +45,32 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
         executeTest("testPoolCaller:"+name+" args=" + args, spec);
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
         PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","0934f72865388999efec64bd9d4a9b93");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
         PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","126581c72d287722437274d41b6fed7b");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
         PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","b543aa1c3efedb301e525c1d6c50ed8d");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
         PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","55b20557a836bb92688e68f12d7f5dc4");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
          PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","7eb889e8e07182f4c3d64609591f9459");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
         PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "db8114877b99b14f7180fdcd24b040a7");
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index f15fa9b99..c9656dd00 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -259,6 +258,16 @@ public class UnifiedGenotyperEngine {
         return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model);
     }
 
+    /**
+     * Compute genotypes at a given locus.
+     *
+     * @param vc         the GL-annotated variant context
+     * @return the VariantCallContext object
+     */
+    public VariantCallContext calculateGenotypes(VariantContext vc) {
+        return calculateGenotypes(null, null, null, null, vc, GenotypeLikelihoodsCalculationModel.Model.valueOf("SNP"), false);
+    }
+
 
     // ---------------------------------------------------------------------------------------------------------
     //
@@ -647,10 +656,8 @@ public class UnifiedGenotyperEngine {
         // if we're genotyping given alleles and we have a requested SNP at this position, do SNP
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
             final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
-            if ( vcInput == null ) {
-                models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
+            if ( vcInput == null )
                 return models;
-            }
 
             if ( vcInput.isSNP() )  {
                 // ignore SNPs if the user chose INDEL mode only
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 0810710c1..f775c8dd6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -568,7 +568,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
 
             if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
-                final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull());
+                final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull());
                 addAnnotations(builder, sub);
                 sub = builder.make();
             }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index e172200f7..bde597fbe 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -148,7 +148,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4")
+                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
         );
 
         executeTest("testRegenotype--" + testFile, spec);