diff --git a/tests/cases/gatk_truncated.vcf.gz b/tests/cases/gatk_truncated.vcf.gz
new file mode 100644
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diff --git a/tests/cases/gatk_truncated.vcf.gz.tbi b/tests/cases/gatk_truncated.vcf.gz.tbi
new file mode 100644
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diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py
index c4e56c0a2ac189363850d26e848d9aa2cd606e16..e4afd85c2b2d573d82deaea7e016eaa27c83de7a 100644
--- a/tests/test_evaluate.py
+++ b/tests/test_evaluate.py
@@ -94,5 +94,42 @@ def NA12878_BLANK():
     return d
 
 
-# def test_no_call2(NA12878_BLANK):
-#     assert NA12878_BLANK['alleles_no_call'] == 8
+@pytest.fixture(scope='module')
+def NA12878_call_truncated():
+    """ When the call set is truncated, i.e. is missing variants which are
+    present in the positive vcf file """
+
+    filename = 'tests/cases/gatk.vcf.gz'
+    truncated = 'tests/cases/gatk_truncated.vcf.gz'
+    call = VCF(truncated, gts012=True)
+    positive = VCF(filename, gts012=True)
+    d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
+                               positive_samples=['BLANK'],
+                               min_gq=30, min_dp=20)
+    return d
+
+
+def test_truncated_called_no_call(NA12878_call_truncated):
+    """ Variants which are missing from the call vcf count towards
+    alleles_no_call """
+    assert NA12878_call_truncated['alleles_no_call'] == 12
+
+
+@pytest.fixture(scope='module')
+def NA12878_positive_truncated():
+    """ When the known set is truncated, i.e. the called vcf file contains
+    variants which are absent from the positive vcf file """
+    filename = 'tests/cases/gatk.vcf.gz'
+    truncated = 'tests/cases/gatk_truncated.vcf.gz'
+    call = VCF(filename, gts012=True)
+    positive = VCF(truncated, gts012=True)
+    d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
+                               positive_samples=['BLANK'],
+                               min_gq=30, min_dp=20)
+    return d
+
+
+def test_truncated_known_no_call(NA12878_positive_truncated):
+    """ Variants which are missing from the known vcf do not count towards
+    alleles_no_call """
+    assert NA12878_positive_truncated['alleles_no_call'] == 0
diff --git a/vtools/evaluate.py b/vtools/evaluate.py
index edb3deff1838243114cc4ad1dcb0fd52cfac4751..f42dc15abae38169ac1915bf9bc0889191445adc 100644
--- a/vtools/evaluate.py
+++ b/vtools/evaluate.py
@@ -83,6 +83,10 @@ def site_concordancy(call_vcf: VCF,
                     and it_record.ALT == pos_record.ALT):
                 same.append(it_record)
 
+        # If the variant is not present in the call vcf
+        if len(same) == 0:
+            d['alleles_no_call'] += 2
+
         if len(same) != 1:
             continue