diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
index 50a9d0a8c..bf91b41c3 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
@@ -101,13 +101,17 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
     protected final GenomeLocParser genomeLocParser;
 
     // the model used for calculating p(non-ref)
-    protected ThreadLocal<AFCalc> afcm = new ThreadLocal<AFCalc>() {
+    protected ThreadLocal<AFCalc> afcm = getAlleleFrequencyCalculatorThreadLocal();
 
-        @Override
-        public AFCalc initialValue() {
-            return AFCalcFactory.createAFCalc(configuration, numberOfGenomes, logger);
-        }
-    };
+    protected ThreadLocal<AFCalc> getAlleleFrequencyCalculatorThreadLocal() {
+        return new ThreadLocal<AFCalc>() {
+
+            @Override
+            public AFCalc initialValue() {
+                return AFCalcFactory.createAFCalc(configuration, numberOfGenomes, false, logger);
+            }
+        };
+    }
 
 
     /**
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java
index ad4ce979a..c291890ff 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java
@@ -151,7 +151,7 @@ public class AFCalcFactory {
      * @return an initialized AFCalc
      */
     public static AFCalc createAFCalc(final StandardCallerArgumentCollection UAC,
-                                      final int nSamples,
+                                      final int nSamples, final boolean emitConfModel,
                                       final Logger logger) {
         final Calculation afCalculationModel = Calculation.getBestModel(UAC.genotypeArgs.samplePloidy,UAC.genotypeArgs.MAX_ALTERNATE_ALLELES,
                 UAC.requestedAlleleFrequencyCalculationModel);
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
index 98df248aa..00a20cc43 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
@@ -163,18 +163,20 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
         final ExactACset set = new ExactACset(1, new ExactACcounts(zeroCounts));
         set.getLog10Likelihoods()[0] = 0.0;
 
+        final int genotypeCount = genotypeLikelihoods.size();
         combinedPoolLikelihoods.add(set);
 
-        if ( genotypeLikelihoods.size() <= 1 ) {
+        getStateTracker().reset(numAlleles - 1);
+        if ( genotypeCount <= 1 ) {
             // no meaningful GLs at all, just set the tracker to non poly values
-            getStateTracker().reset(); // just mimic-ing call below
+            // just mimic-ing call below
             getStateTracker().setLog10LikelihoodOfAFzero(0.0);
         } else {
-            for (int p=1; p<genotypeLikelihoods.size(); p++) {
-                getStateTracker().reset(); // TODO -- why is this here?  It makes it hard to track the n evaluation
+            for (int p=1; p<genotypeCount; p++) {
                 combinedPoolLikelihoods = fastCombineMultiallelicPool(combinedPoolLikelihoods, genotypeLikelihoods.get(p),
                         combinedPloidy, ploidyPerPool, numAlleles, log10AlleleFrequencyPriors);
                 combinedPloidy = ploidyPerPool + combinedPloidy; // total number of chromosomes in combinedLikelihoods
+                if (p < genotypeCount - 1) getStateTracker().reset(); // TODO -- why is this here?  It makes it hard to track the n evaluation
             }
         }
     }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java
index 51f5daffc..27ae69512 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java
@@ -82,8 +82,8 @@ final class StateTracker {
      * maxAltAlleles in length, and so only the first getAllelesUsedInGenotyping.size() - 1 values
      * are meaningful.
      */
-    private final int[] alleleCountsOfMLE;
-    private final int[] alleleCountsOfMAP;
+    private int[] alleleCountsOfMLE;
+    private int[] alleleCountsOfMAP;
 
     /**
      * A vector of log10 likelihood values seen, for future summation.  When the size of the
@@ -227,6 +227,31 @@ final class StateTracker {
     //
     // --------------------------------------------------------------------------------
 
+    /**
+     * Reset the data in this results object, so that it can be used in a subsequent AF calculation
+     *
+     * Resetting of the data is done by the calculation model itself, so shouldn't be done by callers any longer
+     *
+     * @param ensureAltAlleleCapacity indicate the minimum number of alt-alleles that should be supported by the
+     *                                tracker.
+     */
+    protected void reset(final int ensureAltAlleleCapacity) {
+        log10MLE = log10MAP = log10LikelihoodOfAFzero = VALUE_NOT_CALCULATED;
+        log10LikelihoodsForAFGt0CacheIndex = 0;
+        log10LikelihoodsForAFGt0Sum = null;
+        allelesUsedInGenotyping = null;
+        nEvaluations = 0;
+        if (alleleCountsOfMAP.length < ensureAltAlleleCapacity) {
+            final int newCapacity = Math.max(ensureAltAlleleCapacity,alleleCountsOfMAP.length << 1);
+            alleleCountsOfMAP = new int[newCapacity];
+            alleleCountsOfMLE = new int[newCapacity];
+        } else {
+            Arrays.fill(alleleCountsOfMLE, 0);
+            Arrays.fill(alleleCountsOfMAP, 0);
+        }
+        Arrays.fill(log10LikelihoodsForAFGt0, Double.POSITIVE_INFINITY);
+    }
+
     /**
      * Reset the data in this results object, so that it can be used in a subsequent AF calculation
      *
@@ -243,6 +268,7 @@ final class StateTracker {
         Arrays.fill(log10LikelihoodsForAFGt0, Double.POSITIVE_INFINITY);
     }
 
+
     /**
      * Tell this result we used one more evaluation cycle
      */
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 3bb40eaac..2c12b4887 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -68,8 +68,12 @@ import org.broadinstitute.gatk.engine.walkers.*;
 import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.gatk.tools.walkers.genotyper.*;
+import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
 import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
-import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.QualityUtils;
 import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
 import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState;
 import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState;
@@ -623,6 +627,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     public void initialize() {
         super.initialize();
 
+
+
         if (dontGenotype && emitReferenceConfidence())
             throw new UserException("You cannot request gVCF output and do not genotype at the same time");
 
@@ -702,9 +708,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
             headerInfo.add(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"));
         }
 
-        if (SCAC.genotypeArgs.samplePloidy != HomoSapiensConstants.DEFAULT_PLOIDY) {
-            if (SCAC.emitReferenceConfidence != ReferenceConfidenceMode.NONE)
-                throw new UserException.BadArgumentValue("ERC", "For now ploidies different that 2 are not allow for GVCF or BP_RESOLUTION outputs");
+        if (SCAC.genotypeArgs.samplePloidy != HomoSapiensConstants.DEFAULT_PLOIDY || SCAC.requestedAlleleFrequencyCalculationModel == AFCalcFactory.Calculation.EXACT_GENERAL_PLOIDY) {
             headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample"));
             headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample"));
         }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
index 40cf7196c..604c9cd00 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
@@ -51,6 +51,8 @@ import com.google.java.contract.Requires;
 import htsjdk.variant.variantcontext.*;
 import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import org.broadinstitute.gatk.tools.walkers.genotyper.*;
+import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc;
+import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
 import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.GenomeLocParser;
 import org.broadinstitute.gatk.utils.Utils;
@@ -103,6 +105,18 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
         this(configuration,samples,genomeLocParser,false);
     }
 
+    @Override
+    protected ThreadLocal<AFCalc> getAlleleFrequencyCalculatorThreadLocal() {
+        return new ThreadLocal<AFCalc>() {
+
+            @Override
+            public AFCalc initialValue() {
+                return AFCalcFactory.createAFCalc(configuration, numberOfGenomes,
+                        configuration.emitReferenceConfidence != ReferenceConfidenceMode.NONE , logger);
+            }
+        };
+    }
+
     /**
      * Change the merge variant across haplotypes for this engine.
      *
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index b0c157d82..cb77eb762 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -66,12 +66,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "5cc1858896aca6683282f53054bb7a61"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "010a747f5c41ddb7889168e499eb40bb"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "d7dbc1c8e11a277e9db857eb766fd2c6"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "799752d88c4e15e19a953add764d2239"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "fa057b35d6fe9588c2653b6560d6e3c2"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "d10e8907594414890cbf80d282426812"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ea86317a90452eaf7c075f7a3aae77a"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "14e6011cc71541be5a6e70fecf6ce455"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "7e51552ac313840ae16c9b8187b01091"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "a4a89693cc1b5385b17c805a8b655cc0"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1a6d0dc9afd3394ebec99480cb97eb7a"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e462b6527ed9eb1c09261b453a7dadc4"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -103,12 +103,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "6e157b6fdf4071fcb7da74f40146a611"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "354b84dbfaf55947aea40865e74ce66b"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fc4b7e6528747cb20e0c92699a0787cb"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6e0f5d82b77ea79a639d43b2db70e751"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a3daf472f7ab16667e5f6dab1af392ff"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "af9230fa56752b732572ce956101a2be"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "efe4e8e4d28d419e40945a948fd5bdd0"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8deed579c166443851d8fe7e3c521197"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "384e41d7c962e7a9c191c3646239b9f3"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "207ad9fdcc8d557010ec1bf2ae9f65dc"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "d5b914a994b8c2f2d70960bd444fcbba"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "34e76939b6aaa206fa42548a225b15c4"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -128,7 +128,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     /**
      * Example testng test using MyDataProvider
      */
-    @Test(dataProvider = "MyDataProviderHaploid", enabled=false)
+    @Test(dataProvider = "MyDataProviderHaploid", enabled=true)
     public void testHCWithGVCFHaploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
         final String commandLine = String.format("-T HaplotypeCaller -ploidy 1 --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
@@ -140,7 +140,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     /**
      * Example testng test using MyDataProvider
      */
-    @Test(dataProvider = "MyDataProviderTetraploid", enabled=false)
+    @Test(dataProvider = "MyDataProviderTetraploid", enabled=true)
     public void testHCWithGVCFTetraploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
         final String commandLine = String.format("-T HaplotypeCaller -ploidy 4 --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
@@ -219,20 +219,26 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         executeTest("testNoCallGVCFMissingPLsBugFix", spec);
     }
 
-    @Test(enabled=false)
+    /**
+     * Checking that the bug's Exception is no longer been thrown (thus no md5).
+     */
+    @Test(enabled=true)
     public void testGeneralPloidyArrayIndexBug1Fix() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 1 -maxAltAlleles 2 -isr INTERSECTION -L 1:23696115-23696189",
                 b37KGReference, GENERAL_PLOIDY_BUGFIX1_BAM, GENERAL_PLOIDY_BUGFIX1_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7c263d77bf831551366c6e36233b46ce"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
         executeTest(" testGeneralPloidyArrayIndexBug1Fix", spec);
     }
 
-    @Test(enabled=false)
+    /**
+     * Checking that the bug's Exception is no longer been thrown (thus no md5).
+     */
+    @Test(enabled=true)
     public void testGeneralPloidyArrayIndexBug2Fix() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 2 -maxAltAlleles 2 -A DepthPerSampleHC -A StrandBiasBySample -L 1:38052860-38052937",
                 b37KGReference, GENERAL_PLOIDY_BUGFIX2_BAM, GENERAL_PLOIDY_BUGFIX2_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7c263d77bf831551366c6e36233b46ce"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
         executeTest(" testGeneralPloidyArrayIndexBug2Fix", spec);
     }