diff --git a/pom.xml b/pom.xml
index 96074d881..e713df56f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>public/sting-root</relativePath>
     </parent>
 
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index d75c5b056..509f984a3 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
index 6f56415f7..d9b0c575e 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
@@ -48,6 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.vcf.VCFConstants;
@@ -67,14 +68,18 @@ public class PosteriorLikelihoodsUtils {
             throw new IllegalArgumentException("EM loop for posterior GLs not yet implemented");
 
         final Map<Allele,Integer> totalAlleleCounts = new HashMap<>();
+
+        //store the allele counts for each allele in the variant priors
         for ( final VariantContext resource : resources ) {
             addAlleleCounts(totalAlleleCounts,resource,useAC);
         }
 
+        //add the allele counts from the input samples (if applicable)
         if ( useInputSamples ) {
             addAlleleCounts(totalAlleleCounts,vc1,useAC);
         }
 
+        //add zero allele counts for any reference alleles not seen in priors (if applicable)
         totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources);
 
         // now extract the counts of the alleles present within vc1, and in order
@@ -86,6 +91,7 @@ public class PosteriorLikelihoodsUtils {
                     totalAlleleCounts.get(allele) : 0 );
         }
 
+        //parse the likelihoods for each sample's genotype
         final List<double[]> likelihoods = new ArrayList<>(vc1.getNSamples());
         for ( final Genotype genotype : vc1.getGenotypes() ) {
             likelihoods.add(genotype.hasLikelihoods() ? genotype.getLikelihoods().getAsVector() : null );
@@ -196,13 +202,24 @@ public class PosteriorLikelihoodsUtils {
         return priors;
     }
 
+    /**
+     * Parse counts for each allele
+     * @param counts - Map to store and return data
+     * @param context - line to be parsed from the input VCF file
+     * @param useAC - use allele count annotation value from VariantContext (vs. MLEAC)
+     */
     private static void addAlleleCounts(final Map<Allele,Integer> counts, final VariantContext context, final boolean useAC) {
         final int[] ac;
+        //use MLEAC value...
         if ( context.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && ! useAC ) {
-            ac = extractInts(context.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY));
-        } else if ( context.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
-            ac = extractInts(context.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
-        } else {
+            ac = getAlleleCounts(VCFConstants.MLE_ALLELE_COUNT_KEY, context);
+        }
+        //...unless specified by the user in useAC or unless MLEAC is absent
+        else if ( context.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
+            ac = getAlleleCounts(VCFConstants.ALLELE_COUNT_KEY, context);
+        }
+        //if VariantContext annotation doesn't contain AC or MLEAC then get the data from direct evaluation
+        else {
             ac = new int[context.getAlternateAlleles().size()];
             int idx = 0;
             for ( final Allele allele : context.getAlternateAlleles() ) {
@@ -210,24 +227,52 @@ public class PosteriorLikelihoodsUtils {
             }
         }
 
+        //since the allele count for the reference allele is not given in the VCF format,
+        //calculate it from the allele number minus the total counts for alternate alleles
         for ( final Allele allele : context.getAlleles() ) {
             final int count;
             if ( allele.isReference() ) {
                 if ( context.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
-                    count = context.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,-1) - (int) MathUtils.sum(ac);
+                    count = Math.max(context.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,-1) - (int) MathUtils.sum(ac),0); //occasionally an MLEAC value will sneak in that's greater than the AN
                 } else {
-                    count = context.getCalledChrCount() - (int) MathUtils.sum(ac);
+                    count = Math.max(context.getCalledChrCount() - (int) MathUtils.sum(ac),0);
                 }
             } else {
                 count = ac[context.getAlternateAlleles().indexOf(allele)];
             }
+            //if this allele isn't in the map yet, add it
             if ( ! counts.containsKey(allele) ) {
                 counts.put(allele,0);
             }
+            //add the count for the current allele to the existing value in the map
             counts.put(allele,count + counts.get(allele));
         }
     }
 
+    /**
+     * Retrieve allele count data from VariantContext using VCFkey, checks for correct number of values in VCF
+     * @param VCFkey VariantContext annotation tag of interest (should be AC or MLEAC)
+     * @param context VariantContext from which to extract the data
+     * @return int[] with allele count data
+     */
+    private static int[] getAlleleCounts(final String VCFkey, final VariantContext context) {
+        final Object alleleCountsFromVCF = context.getAttribute(VCFkey);
+        if ( alleleCountsFromVCF instanceof List ) {
+            if ( ((List) alleleCountsFromVCF).size() != context.getAlternateAlleles().size() )
+                throw new UserException(String.format("Variant does not contain the same number of MLE allele counts as alternate alleles for record at %s:%d", context.getChr(), context.getStart()));
+        }
+        else if ( alleleCountsFromVCF instanceof String || alleleCountsFromVCF instanceof Integer) {//here length is 1
+            if (context.getAlternateAlleles().size() != 1)
+                throw new UserException(String.format("Variant does not contain the same number of MLE allele counts as alternate alleles for record at %s:%d", context.getChr(), context.getStart()));
+        }
+        return extractInts(alleleCountsFromVCF);
+    }
+
+    /**
+     * Check the formatting on the Object returned by a call to VariantContext::getAttribute() and parse appropriately
+     * @param integerListContainingVCField - Object returned by a call to VariantContext::getAttribute()
+     * @return - array of ints
+     */
     public static int[] extractInts(final Object integerListContainingVCField) {
         List<Integer> mleList = null;
         if ( integerListContainingVCField instanceof List ) {
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
index 50c896450..6ece527ce 100755
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
@@ -135,7 +135,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         metrics.update(eval,truth);
         Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
         Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),1);
@@ -185,7 +185,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         metrics.update(eval,truth);
         Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
         Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
@@ -205,7 +205,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         codec = new VCFCodec();
         evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         metrics.update(eval,truth);
         Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
         Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
@@ -260,7 +260,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         metrics.update(eval,truth);
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample1").getnMismatchingAlt(),1);
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
@@ -313,7 +313,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         metrics.update(eval,truth);
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
@@ -362,7 +362,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         metrics.update(eval,truth);
         Assert.assertTrue(eval.getGenotype("test1_sample2").getType().equals(GenotypeType.UNAVAILABLE));
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
@@ -516,7 +516,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
 
         for ( Pair<VariantContext,VariantContext> contextPair : data ) {
             VariantContext eval = contextPair.getFirst();
@@ -550,7 +550,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
         int[][] table = metrics.getOverallGenotypeConcordance().getTable();
         // set up the table
         table[0] = new int[] {30, 12, 7, 5, 6, 0};
@@ -585,8 +585,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
         VCFHeader disjointCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
         VCFHeader overlapCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
-        ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader);
-        ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader);
+        ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader,false);
+        ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader,false);
 
         // test what happens if you put in disjoint sets and start making requests
         Assert.assertEquals(0,disjointMetrics.getPerSampleGenotypeConcordance().size());
@@ -716,7 +716,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VCFCodec codec = new VCFCodec();
         VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
         VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
-        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
+        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,false);
 
         List<Pair<VariantContext,VariantContext>> data = getData7();
 
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
index 0eca18c46..87f664905 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
@@ -52,6 +52,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
  * Date: 12/8/13
  */
 
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.variant.variantcontext.*;
@@ -192,6 +193,101 @@ public class PosteriorLikelihoodsUtilsUnitTest extends BaseTest {
         Assert.assertEquals(arraysEq(test2exp1.getPL(),_mleparse((List<Integer>) test2result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
     }
 
+    @Test
+     private void testCalculatePosteriorHOM_VARtoHET() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,1,0));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,500).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+
+        int[] GP = _mleparse( (List<Integer>)test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY));
+        Assert.assertTrue(GP[2] > GP[1]);
+    }
+
+    @Test
+    private void testCalculatePosteriorHETtoHOM_VAR() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,0,1));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,900).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+
+        int[] GP = _mleparse( (List<Integer>)test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY));
+        Assert.assertTrue(GP[2] < GP[1]);
+    }
+
+    @Test
+    private void testCalculatePosteriorHOM_REFtoHET() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,0,1,40));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,500).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+
+        int[] GP = _mleparse( (List<Integer>)test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY));
+        Assert.assertTrue(GP[0] > GP[1]);
+    }
+
+    @Test
+    private void testCalculatePosteriorHETtoHOM_REF() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,1,0,40));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,100).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+
+        int[] GP = _mleparse( (List<Integer>)test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY));
+        Assert.assertTrue(GP[0] < GP[1]);
+    }
+
+    @Test
+    private void testMLEACgreaterThanAN() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0),
+                makeG("s2",Aref,T,18,0,24),
+                makeG("s3",Aref,T,22,0,12));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,11).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+    }
+
+    @Test (expectedExceptions = {UserException.class})
+    private void testWrongNumberACvalues() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0),
+                makeG("s2",Aref,T,18,0,24),
+                makeG("s3",Aref,T,22,0,12));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T,C))).attribute(VCFConstants.ALLELE_COUNT_KEY,5).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make());
+
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+    }
+
+    @Test (expectedExceptions = {UserException.class})
+    private void testWrongNumberMLEACvalues() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0),
+                makeG("s2",Aref,T,18,0,24),
+                makeG("s3",Aref,T,22,0,12));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T,C))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,5).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+    }
+
+    @Test
+    private void testMultipleACvalues() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0),
+                makeG("s2",Aref,T,18,0,24),
+                makeG("s3",Aref,T,22,0,12));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T,C))).attribute(VCFConstants.ALLELE_COUNT_KEY,Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+    }
+
+    @Test
+    private void testMultipleMLEACvalues() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0),
+                makeG("s2",Aref,T,18,0,24),
+                makeG("s3",Aref,T,22,0,12));
+        List<VariantContext> supplTest1 = new ArrayList<>(1);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T,C))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make());
+        VariantContext test1result = PosteriorLikelihoodsUtils.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+    }
+
     private double[] pl2gl(int[] pl) {
         double[] gl = new double[pl.length];
         for ( int idx = 0; idx < gl.length; idx++ ) {
diff --git a/protected/pom.xml b/protected/pom.xml
index 4b165d477..261bb42f8 100644
--- a/protected/pom.xml
+++ b/protected/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../public/sting-root</relativePath>
     </parent>
 
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index bdfeb099f..e8889787f 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -9,7 +9,7 @@
     <name>GATK External Example</name>
 
     <properties>
-        <sting.version>2.8-SNAPSHOT</sting.version>
+        <sting.version>3.1-SNAPSHOT</sting.version>
         <!--
         sting.basedir property must point to your checkout of Sting/GATK until we can get all the
         dependencies out of the committed sting repo and into central.
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index 6b82c8618..068c062a7 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
index 848261d73..395e24604 100755
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
@@ -42,8 +42,9 @@ public class ConcordanceMetrics {
     private Map<String,GenotypeConcordanceTable> perSampleGenotypeConcordance;
     private GenotypeConcordanceTable overallGenotypeConcordance;
     private SiteConcordanceTable overallSiteConcordance;
+    private boolean printInterestingSites;
 
-    public ConcordanceMetrics(VCFHeader evaluate, VCFHeader truth) {
+    public ConcordanceMetrics(VCFHeader evaluate, VCFHeader truth, boolean printSitesEnabled) {
         HashSet<String> overlappingSamples = new HashSet<String>(evaluate.getGenotypeSamples());
         overlappingSamples.retainAll(truth.getGenotypeSamples());
         perSampleGenotypeConcordance = new HashMap<String, GenotypeConcordanceTable>(overlappingSamples.size());
@@ -52,6 +53,7 @@ public class ConcordanceMetrics {
         }
         overallGenotypeConcordance = new GenotypeConcordanceTable();
         overallSiteConcordance = new SiteConcordanceTable();
+        printInterestingSites = printSitesEnabled;
     }
 
     public GenotypeConcordanceTable getOverallGenotypeConcordance() {
@@ -114,6 +116,7 @@ public class ConcordanceMetrics {
 
     @Requires({"eval != null","truth != null"})
     public void update(VariantContext eval, VariantContext truth) {
+        boolean doPrint = false;
         overallSiteConcordance.update(eval,truth);
         Set<String> alleleTruth = new HashSet<String>(8);
         String truthRef = truth.getReference().getBaseString();
@@ -130,7 +133,12 @@ public class ConcordanceMetrics {
                 throw new UserException(String.format("Concordance Metrics is currently only implemented for DIPLOID genotypes, found eval ploidy: %d, comp ploidy: %d",evalGenotype.getPloidy(),truthGenotype.getPloidy()));
             }
             perSampleGenotypeConcordance.get(sample).update(evalGenotype,truthGenotype,alleleTruth,truthRef);
-            overallGenotypeConcordance.update(evalGenotype,truthGenotype,alleleTruth,truthRef);
+            doPrint = overallGenotypeConcordance.update(evalGenotype,truthGenotype,alleleTruth,truthRef);
+            if(printInterestingSites && doPrint)
+                System.out.println(eval.getChr() + ":" + eval.getStart() + "\t truth is:" + truthGenotype.getType() + "\t eval is:" + evalGenotype.getType());
+
+                //Below is code to print out mismatched alternate alleles
+                //System.out.println(eval.getChr() + ":" + eval.getStart() + "\t truth is:" + truthGenotype.getAlleles() + "\t eval is:" + evalGenotype.getAlleles());
         }
     }
 
@@ -212,13 +220,14 @@ public class ConcordanceMetrics {
         }
 
         @Requires({"eval!=null","truth != null","truthAlleles != null"})
-        public void update(Genotype eval, Genotype truth, Set<String> truthAlleles, String truthRef) {
+        public Boolean update(Genotype eval, Genotype truth, Set<String> truthAlleles, String truthRef) {
             // this is slow but correct.
 
             // NOTE: a reference call in "truth" is a special case, the eval can match *any* of the truth alleles
             // that is, if the reference base is C, and a sample is C/C in truth, A/C, A/A, T/C, T/T will
             // all match, so long as A and T are alleles in the truth callset.
             boolean matchingAlt = true;
+            int evalGT, truthGT;
             if ( eval.isCalled() && truth.isCalled() && truth.isHomRef() ) {
                 // by default, no-calls "match" between alleles, so if
                 // one or both sites are no-call or unavailable, the alt alleles match
@@ -241,10 +250,17 @@ public class ConcordanceMetrics {
             }
 
             if ( matchingAlt ) {
-                genotypeCounts[eval.getType().ordinal()][truth.getType().ordinal()]++;
+                evalGT = eval.getType().ordinal();
+                truthGT = truth.getType().ordinal();
+                genotypeCounts[evalGT][truthGT]++;
+                if(evalGT != truthGT)  //report variants where genotypes don't match
+                    return true;
             } else {
                 nMismatchingAlt++;
+                return false;
+                //return true; //alternatively, report variants where alt alleles don't match
             }
+            return false;
         }
 
         public int[][] getTable() {
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
index 8c8961cb5..08c938583 100755
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
@@ -25,10 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -213,6 +210,16 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
     @Argument(shortName="moltenize",fullName="moltenize",doc="Molten rather than tabular output")
     public boolean moltenize = false;
 
+    /**
+     * Print sites where genotypes are mismatched between callsets along with annotations giving the genotype of each callset
+     * Outputs directly to System.out.  Super classy.
+     *
+     * NOTE: doesn't currently differentiate between samples, so there may be repeats
+     */
+    @Hidden
+    @Argument(shortName="sites", fullName = "printInterestingSites", required=false)
+    protected boolean printSites = false;
+
     @Output
     PrintStream out;
 
@@ -244,7 +251,7 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
         evalSamples = evalHeader.getGenotypeSamples();
         VCFHeader compHeader = headerMap.get(compBinding.getName());
         compSamples = compHeader.getGenotypeSamples();
-        return new ConcordanceMetrics(evalHeader,compHeader);
+        return new ConcordanceMetrics(evalHeader,compHeader, printSites);
     }
 
 
@@ -347,8 +354,10 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
     }
 
     public ConcordanceMetrics reduce(List<Pair<VariantContext,VariantContext>> evalCompList, ConcordanceMetrics metrics) {
-        for ( Pair<VariantContext,VariantContext> evalComp : evalCompList)
+        for ( Pair<VariantContext,VariantContext> evalComp : evalCompList){
             metrics.update(evalComp.getFirst(),evalComp.getSecond());
+
+        }
         return metrics;
     }
 
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
index 6948c4f3c..29305af3f 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
@@ -58,10 +58,10 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
-    @Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true)
+    @Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=false, exclusiveOf = "splitToManyFiles")
     protected VariantContextWriter vcfWriter1 = null;
 
-    @Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=true)
+    @Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=false, exclusiveOf = "splitToManyFiles")
     // there's a reported bug in the GATK where we can't have 2 @Output writers
     protected File file2 = null;
     protected VariantContextWriter vcfWriter2 = null;
@@ -69,6 +69,17 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="fractionToOut1", shortName="fraction", doc="Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2", required=false)
     protected double fraction = 0.5;
 
+    @Argument(fullName="splitToManyFiles", shortName = "splitToMany", doc="split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required", required = false)
+    protected boolean splitToMany = false;
+
+    @Argument(fullName = "numOfOutputVCFFiles", shortName = "N", doc = "number of output VCF files. Only works with SplitToMany = true", required = false, maxRecommendedValue = 20, minValue = 2)
+    protected int numOfFiles = -1;
+
+    @Argument(fullName = "prefixForAllOutputFileNames", shortName = "baseOutputName", doc = "the name of the output VCF file will be: <baseOutputName>.split.<number>.vcf. Required with SplitToMany option", required = false)
+    protected String baseFileName = null;
+
+    private VariantContextWriter[] writers = null;
+
     /**
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
      */
@@ -76,15 +87,37 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         if ( fraction < 0.0 || fraction > 1.0 )
             throw new UserException.BadArgumentValue("fractionToOut1", "this value needs to be a number between 0 and 1");
 
+        if (splitToMany){
+            if (numOfFiles < 2)
+                throw new UserException.BadArgumentValue("numOfFiles", "this value must be greater than 2 when using the splitToMany option");
+            if (baseFileName == null)
+                throw new UserException.BadArgumentValue("baseFileName", "this value cannot be null (unprovided) when using the splitToMany option");
+        }
+        else{
+            if(vcfWriter1 == null || vcfWriter2 == null)
+                throw new UserException.BadArgumentValue("out1 or out2", "this value cannot be null (unprovided) unless you are using the splitToMany option");
+        }
+
         // setup the header info
         final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
-        Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
-        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        final Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
+        final Set<VCFHeaderLine> hInfo = new HashSet<>();
         hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
 
-        vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
-        vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary());
-        vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
+
+        if(splitToMany){
+            writers = new VariantContextWriter[numOfFiles];
+            for(int i = 0; i<writers.length; i++){
+                writers[i] = VariantContextWriterFactory.create(new File(baseFileName+".split."+i+".vcf"), getMasterSequenceDictionary());
+                writers[i].writeHeader(new VCFHeader(hInfo,samples));
+            }
+
+        }
+        else {
+            vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
+            vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary());
+            vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
+        }
     }
 
     /**
@@ -95,17 +128,23 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
      * @param  context   alignment info
      * @return 1 if the record was printed to the output file, 0 if otherwise
      */
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
-        for ( VariantContext vc : vcs ) {
-            double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble();
-            if ( random < fraction )
-                vcfWriter1.add(vc);
-            else
-                vcfWriter2.add(vc);
+        final Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
+        for ( final VariantContext vc : vcs ) {
+            final double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble();
+            if(splitToMany){
+                final int index = (int)(numOfFiles * random);
+                writers[index].add(vc);
+            }
+            else{
+                if ( random < fraction )
+                    vcfWriter1.add(vc);
+                else
+                    vcfWriter2.add(vc);
+            }
         }
 
         return 1;
@@ -113,10 +152,14 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
 
     public Integer reduceInit() { return 0; }
 
-    public Integer reduce(Integer value, Integer sum) { return value + sum; }
+    public Integer reduce(final Integer value, final Integer sum) { return value + sum; }
 
-    public void onTraversalDone(Integer result) {
+    public void onTraversalDone(final Integer result) {
         logger.info(result + " records processed.");
-        vcfWriter2.close();
+        if(splitToMany)
+            for(final VariantContextWriter writer: writers)
+                writer.close();
+        else
+            vcfWriter2.close();
     }
 }
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 9272cf983..6a8ce94af 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/gatk-queue-extgen/pom.xml b/public/gatk-queue-extgen/pom.xml
index 532515ff8..252a4b33f 100644
--- a/public/gatk-queue-extgen/pom.xml
+++ b/public/gatk-queue-extgen/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml
index 66845f584..a434a1a64 100644
--- a/public/gsalib/pom.xml
+++ b/public/gsalib/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 6d7e356cb..38ef796ae 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../sting-root</relativePath>
     </parent>
 
diff --git a/public/pom.xml b/public/pom.xml
index 89d49997c..0cf40a052 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>sting-root</relativePath>
     </parent>
 
@@ -19,7 +19,7 @@
         <module>sting-utils</module>
         <module>gatk-framework</module>
         <module>gatk-package</module>
-        <module>external-example</module>
+ <!--       <module>external-example</module>  -->
         <!-- queue optionally enabled as profiles -->
     </modules>
 
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index 670750fd0..40c1ad5f0 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index 27b6fae6d..4ff9a1381 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index 549a99ae6..44644e13d 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -12,7 +12,7 @@
 
     <groupId>org.broadinstitute.sting</groupId>
     <artifactId>sting-root</artifactId>
-    <version>2.8-SNAPSHOT</version>
+    <version>3.1-SNAPSHOT</version>
     <packaging>pom</packaging>
     <name>Sting Root</name>
 
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index 7d7ae87b4..c2e680e73 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.8-SNAPSHOT</version>
+        <version>3.1-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>