diff --git a/src/main/java/htsjdk/variant/variantcontext/VariantContext.java b/src/main/java/htsjdk/variant/variantcontext/VariantContext.java
index a6b8a5fce5..55825fb4d7 100644
--- a/src/main/java/htsjdk/variant/variantcontext/VariantContext.java
+++ b/src/main/java/htsjdk/variant/variantcontext/VariantContext.java
@@ -25,7 +25,6 @@
 
 package htsjdk.variant.variantcontext;
 
-import htsjdk.samtools.util.Tuple;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.util.ParsingUtils;
@@ -263,7 +262,7 @@ public class VariantContext implements Feature, Serializable {
 * @return an ordered list of genotype fields in use in VC.  If vc has genotypes this will always include GT first
 */
     public List<String> calcVCFGenotypeKeys(final VCFHeader header) {
-        final Set<String> keys = new HashSet<String>();
+        final Set<String> keys = new HashSet<>();
 
         boolean sawGoodGT = false;
         boolean sawGoodQual = false;
@@ -287,11 +286,11 @@ public List<String> calcVCFGenotypeKeys(final VCFHeader header) {
         if ( sawPL ) keys.add(VCFConstants.GENOTYPE_PL_KEY);
         if ( sawGenotypeFilter ) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
 
-        List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
+        List<String> sortedList = ParsingUtils.sortList(new ArrayList<>(keys));
 
         // make sure the GT is first
         if (sawGoodGT) {
-            final List<String> newList = new ArrayList<String>(sortedList.size()+1);
+            final List<String> newList = new ArrayList<>(sortedList.size() + 1);
             newList.add(VCFConstants.GENOTYPE_KEY);
             newList.addAll(sortedList);
             sortedList = newList;
@@ -434,7 +433,7 @@ public VariantContext subContextFromSamples(Set<String> sampleNames, final boole
                 Set<Allele> allelesFromGenotypes = allelesOfGenotypes(newGenotypes);
 
                 // ensure original order of genotypes
-                List<Allele> rederivedAlleles = new ArrayList<Allele>(allelesFromGenotypes.size());
+                List<Allele> rederivedAlleles = new ArrayList<>(allelesFromGenotypes.size());
                 for (Allele allele : alleles)
                     if (allelesFromGenotypes.contains(allele))
                         rederivedAlleles.add(allele);
@@ -469,7 +468,7 @@ public VariantContext subContextFromSample(String sampleName) {
      * @return allele set
      */
     private final Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) {
-        final Set<Allele> alleles = new HashSet<Allele>();
+        final Set<Allele> alleles = new HashSet<>();
 
         boolean addedref = false;
         for ( final Genotype g : genotypes ) {
@@ -863,7 +862,7 @@ public List<Integer> getIndelLengths() {
             return null;
         }
 
-        List<Integer> lengths = new ArrayList<Integer>();
+        List<Integer> lengths = new ArrayList<>();
         for ( Allele a : getAlternateAlleles() ) {
             lengths.add(a.length() - getReference().length());
         }
@@ -973,7 +972,7 @@ public GenotypesContext getGenotypes(String sampleName) {
      * @throws IllegalArgumentException if sampleName isn't bound to a genotype
      */
     protected GenotypesContext getGenotypes(Collection<String> sampleNames) {
-        return getGenotypes().subsetToSamples(new HashSet<String>(sampleNames));
+        return getGenotypes().subsetToSamples(new HashSet<>(sampleNames));
     }
 
     public GenotypesContext getGenotypes(Set<String> sampleNames) {
@@ -1049,7 +1048,7 @@ public int getCalledChrCount(Set<String> sampleIds) {
      * @return chromosome count
      */
     public int getCalledChrCount(Allele a) {
-        return getCalledChrCount(a,new HashSet<String>(0));
+        return getCalledChrCount(a, new HashSet<>(0));
     }
 
     /**
@@ -1162,7 +1161,7 @@ public int getMixedCount() {
      * Run all extra-strict validation tests on a Variant Context object
      *
      * @param reportedReference   the reported reference allele
-     * @param observedReference   the actual reference allele
+     * @param observedReference     the observed reference allele
      * @param rsIDs               the true dbSNP IDs
      */
     public void extraStrictValidation(final Allele reportedReference, final Allele observedReference, final Set<String> rsIDs) {
@@ -1172,7 +1171,7 @@ public void extraStrictValidation(final Allele reportedReference, final Allele o
         // validate the RS IDs
         validateRSIDs(rsIDs);
 
-        // validate the altenate alleles
+        // validate the alternate alleles
         validateAlternateAlleles();
 
         // validate the AN and AC fields
@@ -1201,7 +1200,7 @@ public void validateAlternateAlleles() {
         if ( !hasGenotypes() )
             return;
 
-        // maintain a list of non-symbolic alleles reported in the REF and ALT fields of the record
+        // maintain a list of non-symbolic alleles expected in the REF and ALT fields of the record
         // (we exclude symbolic alleles because it's commonly expected that they don't show up in the genotypes, e.g. with GATK gVCFs)
         final List<Allele> reportedAlleles = new ArrayList<Allele>();
         for ( final Allele allele : getAlleles() ) {
@@ -1210,7 +1209,7 @@ public void validateAlternateAlleles() {
         }
 
         // maintain a list of non-symbolic alleles observed in the genotypes
-        final Set<Allele> observedAlleles = new HashSet<Allele>();
+        final Set<Allele> observedAlleles = new HashSet<>();
         observedAlleles.add(getReference());
         for ( final Genotype g : getGenotypes() ) {
             if ( g.isCalled() ) {
@@ -1233,24 +1232,39 @@ public void validateAlternateAlleles() {
             throw new TribbleException.InternalCodecException(String.format("one or more of the ALT allele(s) for the record at position %s:%d are not observed at all in the sample genotypes", getContig(), getStart()));
     }
 
+    private void validateAttributeIsExpectedSize(final String attributeKey, final int numAlternateAlleles ) {
+        final List<Object> actualValues = getAttributeAsList(attributeKey);
+        if (!actualValues.isEmpty()) {
+            // always have at least one actual value
+            final int expectedValuesSize = numAlternateAlleles > 0 ? numAlternateAlleles : 1;
+            if (actualValues.size() != expectedValuesSize) {
+                throw new TribbleException.InternalCodecException(String.format("the %s tag has the incorrect number of records at position %s:%d, %d vs. %d", attributeKey, getContig(), getStart(), actualValues.size(), expectedValuesSize));
+            }
+        }
+    }
+
     public void validateChromosomeCounts() {
+        final int numberOfAlternateAlleles = alleles.size() - 1;
+        validateAttributeIsExpectedSize(VCFConstants.ALLELE_COUNT_KEY, numberOfAlternateAlleles);
+        validateAttributeIsExpectedSize(VCFConstants.ALLELE_FREQUENCY_KEY, numberOfAlternateAlleles);
+
         if ( !hasGenotypes() )
             return;
 
         // AN
         if ( hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
-            int reportedAN = Integer.valueOf(getAttribute(VCFConstants.ALLELE_NUMBER_KEY).toString());
-            int observedAN = getCalledChrCount();
+            final int reportedAN = Integer.valueOf(getAttribute(VCFConstants.ALLELE_NUMBER_KEY).toString());
+            final int observedAN = getCalledChrCount();
             if ( reportedAN != observedAN )
                 throw new TribbleException.InternalCodecException(String.format("the Allele Number (AN) tag is incorrect for the record at position %s:%d, %d vs. %d", getContig(), getStart(), reportedAN, observedAN));
         }
 
         // AC
         if ( hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
-            ArrayList<Integer> observedACs = new ArrayList<Integer>();
+            final ArrayList<Integer> observedACs = new ArrayList<>();
 
             // if there are alternate alleles, record the relevant tags
-            if (!getAlternateAlleles().isEmpty()) {
+            if ( numberOfAlternateAlleles > 0 ) {
                 for ( Allele allele : getAlternateAlleles() ) {
                     observedACs.add(getCalledChrCount(allele));
                 }
@@ -1259,22 +1273,13 @@ public void validateChromosomeCounts() {
                 observedACs.add(0);
             }
 
-            if ( getAttribute(VCFConstants.ALLELE_COUNT_KEY) instanceof List ) {
-                final List reportedACs = (List)getAttribute(VCFConstants.ALLELE_COUNT_KEY);
-                if ( observedACs.size() != reportedACs.size() )
-                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have the correct number of values for the record at position %s:%d, %d vs. %d", getContig(), getStart(), reportedACs.size(), observedACs.size()));
-                for (int i = 0; i < observedACs.size(); i++) {
-                    // need to cast to int to make sure we don't have an issue below with object equals (earlier bug) - EB
-                    final int reportedAC = Integer.valueOf(reportedACs.get(i).toString());
-                    if ( reportedAC != observedACs.get(i) )
-                        throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %s vs. %d", getContig(), getStart(), reportedAC, observedACs.get(i)));
-                }
-            } else {
-                if ( observedACs.size() != 1 )
-                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have enough values for the record at position %s:%d", getContig(), getStart()));
-                int reportedAC = Integer.valueOf(getAttribute(VCFConstants.ALLELE_COUNT_KEY).toString());
-                if ( reportedAC != observedACs.get(0) )
-                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %d vs. %d", getContig(), getStart(), reportedAC, observedACs.get(0)));
+            final List<Object> reportedACs = getAttributeAsList(VCFConstants.ALLELE_COUNT_KEY);
+
+            for (int i = 0; i < observedACs.size(); i++) {
+                // need to cast to int to make sure we don't have an issue below with object equals (earlier bug) - EB
+                final int reportedAC = Integer.valueOf(reportedACs.get(i).toString());
+                if ( reportedAC != observedACs.get(i) )
+                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %s vs. %d", getContig(), getStart(), reportedAC, observedACs.get(i)));
             }
         }
     }
@@ -1473,7 +1478,7 @@ public String toStringWithoutGenotypes() {
 
     // protected basic manipulation routines
     private static List<Allele> makeAlleles(Collection<Allele> alleles) {
-        final List<Allele> alleleList = new ArrayList<Allele>(alleles.size());
+        final List<Allele> alleleList = new ArrayList<>(alleles.size());
 
         boolean sawRef = false;
         for ( final Allele a : alleles ) {
@@ -1544,7 +1549,7 @@ private final void fullyDecodeInfo(final VariantContextBuilder builder, final VC
     private final Map<String, Object> fullyDecodeAttributes(final Map<String, Object> attributes,
                                                             final VCFHeader header,
                                                             final boolean lenientDecoding) {
-        final Map<String, Object> newAttributes = new HashMap<String, Object>(10);
+        final Map<String, Object> newAttributes = new HashMap<>(10);
 
         for ( final Map.Entry<String, Object> attr : attributes.entrySet() ) {
             final String field = attr.getKey();
@@ -1582,7 +1587,7 @@ private final Object decodeValue(final String field, final Object value, final V
             final String string = (String)value;
             if ( string.indexOf(',') != -1 ) {
                 final String[] splits = string.split(",");
-                final List<Object> values = new ArrayList<Object>(splits.length);
+                final List<Object> values = new ArrayList<>(splits.length);
                 for ( int i = 0; i < splits.length; i++ )
                     values.add(decodeOne(field, splits[i], format));
                 return values;
@@ -1591,7 +1596,7 @@ private final Object decodeValue(final String field, final Object value, final V
             }
         } else if ( value instanceof List && (((List) value).get(0)) instanceof String ) {
             final List<String> asList = (List<String>)value;
-            final List<Object> values = new ArrayList<Object>(asList.size());
+            final List<Object> values = new ArrayList<>(asList.size());
             for ( final String s : asList )
                 values.add(decodeOne(field, s, format));
             return values;
diff --git a/src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java b/src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java
index 2dc345fedb..14056f833b 100644
--- a/src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java
+++ b/src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java
@@ -1259,13 +1259,34 @@ public Object[][] testValidateChromosomeCountsDataProvider() {
         final VariantContext vcACSetTwoAlts =
                 createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACTwoAlts, hetVarTC);
 
+        // with AC set, and two different ALTs (T and C), with no GT, we expect a 2 count values.
+        final Map<String, Object> attributesACNoGtTwoAlts = new HashMap<String, Object>();
+        attributesACNoGtTwoAlts.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1", "1"));
+        final VariantContext vcACNoGtSetTwoAlts =
+                createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACNoGtTwoAlts, null);
+
+        // with AF set, and two different ALTs (T and C), with GT of 1/2, we expect two frequncy values.
+        // With two ALTs, a list is expected, so we set the attribute as a list of 0.5,0.5
+        final Map<String, Object> attributesAFTwoAlts = new HashMap<String, Object>();
+        attributesAFTwoAlts.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5", "0.5"));
+        final VariantContext vcAFSetTwoAlts =
+                createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFTwoAlts, hetVarTC);
+
+        // with AF set, and two different ALTs (T and C), with no GT, we expect two frequency values.
+        final Map<String, Object> attributesAFNoGtTwoAlts = new HashMap<String, Object>();
+        attributesAFNoGtTwoAlts.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5", "0.5"));
+        final VariantContext vcAFNoGtSetTwoAlts =
+                createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFNoGtTwoAlts, null);
+
         return new Object[][]{
                 {vcNoGenotypes},
                 {vcANSet},
                 {vcANSetNoCall},
                 {vcACSet},
                 {vcACSetNoAlts},
-                {vcACSetTwoAlts}
+                {vcACNoGtSetTwoAlts},
+                {vcAFSetTwoAlts},
+                {vcAFNoGtSetTwoAlts}
         };
     }
     @Test(dataProvider = "testValidateChromosomeCountsDataProvider")
@@ -1319,13 +1340,34 @@ public Object[][] testValidateChromosomeCountsFailureDataProvider() {
         final VariantContext vcACSetTwoAltsOneAltCount =
                 createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACTwoAltsOneAltCount, hetVarTC);
 
+        // with AC set, no GT, two ALTs, but only count for one ALT (we expect two items in the list: 1,1)
+        final Map<String, Object> attributesACNoGtTwoAltsOneAltCount = new HashMap<String, Object>();
+        attributesACNoGtTwoAltsOneAltCount.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1"));
+        final VariantContext vcACNoGtSetTwoAltsOneAltCount =
+                createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACNoGtTwoAltsOneAltCount, null);
+
+        // with AF set, two ALTs, but only frequency for one ALT (we expect two items in the list
+        final Map<String, Object> attributesAFTwoAltsWrongFreq = new HashMap<String, Object>();
+        attributesAFTwoAltsWrongFreq.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5"));
+        final VariantContext vcAFSetTwoAltsWrongFreq =
+                createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFTwoAltsWrongFreq, hetVarTC);
+
+        // with AF set, no GT, two ALTs, but only frequency for one ALT (we expect two items in the list
+        final Map<String, Object> attributesAFNoGtTwoAltsWrongCount = new HashMap<String, Object>();
+        attributesAFNoGtTwoAltsWrongCount.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5"));
+        final VariantContext vcAFNoGtSetTwoAltsWrongFreq =
+                createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFNoGtTwoAltsWrongCount, null);
+
         return new Object[][]{
                 {vcANSet},
                 {vcANSetNoCall},
                 {vcACWrongCount},
                 {vcACSetTwoAlts},
                 {vcACSetTwoAltsWrongCount},
-                {vcACSetTwoAltsOneAltCount}
+                {vcACSetTwoAltsOneAltCount},
+                {vcACNoGtSetTwoAltsOneAltCount},
+                {vcAFSetTwoAltsWrongFreq},
+                {vcAFNoGtSetTwoAltsWrongFreq}
         };
     }
     @Test(dataProvider = "testValidateChromosomeCountsFailureDataProvider", expectedExceptions = TribbleException.class)