diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/CombinationUtil.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/CombinationUtil.java
index 6adcc9a5..1c8c10cb 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/CombinationUtil.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/CombinationUtil.java
@@ -22,10 +22,25 @@ public static Set<String> generatePermutations(List<SampleAllele> alleles) {
     Preconditions.checkNotNull(alleles);
     Preconditions.checkArgument(!alleles.isEmpty(), "No alleles to generate permutations for");
 
-    boolean isHaploid = alleles.stream().allMatch(sa -> sa.getAllele2() == null);
-    Set<String> rez = generatePermutations(alleles, 0, isHaploid, true, "");
-    if (!isHaploid) {
-      rez.addAll(generatePermutations(alleles, 0, false, false, ""));
+    boolean isS1Blank = true;
+    boolean isS2Blank = true;
+    for (SampleAllele sa : alleles) {
+      if (sa.getAllele1() != null) {
+        isS1Blank = false;
+      }
+      if (sa.getAllele2() != null) {
+        isS2Blank = false;
+      }
+      if (!isS1Blank && !isS2Blank) {
+        break;
+      }
+    }
+    Set<String> rez = new HashSet<>();
+    if (!isS1Blank) {
+      rez.addAll(generatePermutations(alleles, 0, isS2Blank, true, ""));
+    }
+    if (!isS2Blank) {
+      rez.addAll(generatePermutations(alleles, 0, isS1Blank, false, ""));
     }
     if (rez.isEmpty()) {
       throw new IllegalStateException("No permutations generated from " + alleles.size() + " alleles");
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java
index bd493b57..6ede8b5a 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/DpydHapB3Matcher.java
@@ -70,59 +70,71 @@ public DpydHapB3Matcher(Env env, SortedMap<String, SampleAllele> alleleMap, bool
       m_isMissingHapB3 = false;
       if (hapB3IntronSample != null) {
         List<String> intronicHapB3 = callHapB3(hapB3Allele, hapB3IntronLocus, hapB3IntronSample);
+        long numIntronicStrands = intronicHapB3.stream().filter(a -> !a.equals(".")).count();
 
         if (hapB3ExonSample == null) {
           m_hapB3IntronCall = intronicHapB3;
         } else {
           // we have both intron and exon variants
           List<String> exonicHapB3 = callHapB3(hapB3Allele, hapB3ExonLocus, hapB3ExonSample);
+          long numExonicStrands = exonicHapB3.stream().filter(a -> !a.equals(".")).count();
 
-          if (intronicHapB3.isEmpty()) {
+          if (numIntronicStrands == 0) {
             m_hapB3Call = exonicHapB3;
-            if (!exonicHapB3.isEmpty()) {
+            if (numExonicStrands != 0) {
               m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
             }
-          } else if (intronicHapB3.size() == 1) {
-            // ignore this case
-          } else if (intronicHapB3.size() == 2) {
-            if (exonicHapB3.isEmpty()) {
+          } else if (numIntronicStrands == 1) {
+            if (numExonicStrands == 0) {
               m_hapB3IntronCall = intronicHapB3;
-            } else if (exonicHapB3.size() == 1) {
-              // ignore this case
-            } else if (exonicHapB3.size() == 2) {
-              m_hapB3IntronCall = new ArrayList<>();
-              m_hapB3Call = new ArrayList<>();
+            } else {
+              // ignore if not phased
               if (isEffectivelyPhased) {
-                handlePhasedCall(env, intronicHapB3.get(0), exonicHapB3.get(0));
-                handlePhasedCall(env, intronicHapB3.get(1), exonicHapB3.get(1));
+                handlePhasedCall(env, intronicHapB3, exonicHapB3, 0);
+                handlePhasedCall(env, intronicHapB3, exonicHapB3, 1);
+              }
+            }
+          } else if (numIntronicStrands == 2) {
+            if (numExonicStrands == 0) {
+              m_hapB3IntronCall = intronicHapB3;
+            } else {
+              if (isEffectivelyPhased) {
+                handlePhasedCall(env, intronicHapB3, exonicHapB3, 0);
+                handlePhasedCall(env, intronicHapB3, exonicHapB3, 1);
               } else {
-                long numIntrons = intronicHapB3.stream().filter(c -> c.equals("1")).count();
-                long numExons = exonicHapB3.stream().filter(c -> c.equals("1")).count();
-
-                if (numIntrons == numExons) {
-                  for (int x = 0; x < numIntrons; x += 1) {
-                    m_hapB3Call.add("1");
-                  }
-                } else if (numIntrons > numExons) {
-                  // 2 intron, 1 exon
-                  // 2 intron, 0 exon
-                  // 1 intron, 0 exon
-                  m_hapB3IntronCall.add("1");
-                  if (numExons == 1) {
-                    m_hapB3Call.add("1");
-                  } else if (numIntrons == 2) {
+                if (numExonicStrands == 1) {
+                  // ignore this case
+                } else if (numExonicStrands == 2) {
+                  m_hapB3IntronCall = new ArrayList<>();
+                  m_hapB3Call = new ArrayList<>();
+                  long numIntronic = intronicHapB3.stream().filter(c -> c.equals("1")).count();
+                  long numExonic = exonicHapB3.stream().filter(c -> c.equals("1")).count();
+
+                  if (numIntronic == numExonic) {
+                    for (int x = 0; x < numIntronic; x += 1) {
+                      m_hapB3Call.add("1");
+                    }
+                  } else if (numIntronic > numExonic) {
+                    // 2 intron, 1 exon
+                    // 2 intron, 0 exon
+                    // 1 intron, 0 exon
                     m_hapB3IntronCall.add("1");
-                  }
-                } else {
-                  // intronic call trumps exonic call
-                  if (numIntrons == 1) {
-                    // 2 exons, 1 intron - call ref/hapB3
-                    m_hapB3Call.add("1");
-                    m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
+                    if (numExonic == 1) {
+                      m_hapB3Call.add("1");
+                    } else if (numIntronic == 2) {
+                      m_hapB3IntronCall.add("1");
+                    }
                   } else {
-                    // 1 exon, 0 intron - call reference
-                    // 2 exon, 0 intron - call reference
-                    m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
+                    // intronic call trumps exonic call
+                    if (numIntronic == 1) {
+                      // 2 exons, 1 intron - call ref/hapB3
+                      m_hapB3Call.add("1");
+                      m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
+                    } else {
+                      // 1 exon, 0 intron - call reference
+                      // 2 exon, 0 intron - call reference
+                      m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
+                    }
                   }
                 }
               }
@@ -131,7 +143,8 @@ public DpydHapB3Matcher(Env env, SortedMap<String, SampleAllele> alleleMap, bool
         }
       } else {
         m_hapB3Call = callHapB3(hapB3Allele, hapB3ExonLocus, hapB3ExonSample);
-        if (m_hapB3Call.size() == 2) {
+        long numAlleles = m_hapB3Call.stream().filter(a -> !a.equals(".")).count();
+        if (numAlleles == 2) {
           m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_EXONIC_ONLY);
         }
       }
@@ -146,7 +159,25 @@ public DpydHapB3Matcher(Env env, SortedMap<String, SampleAllele> alleleMap, bool
     m_isHapB3Present = m_numHapB3Called > 0;
   }
 
-  private void handlePhasedCall(Env env, String intronicCall, String exonicCall) {
+
+  private void handlePhasedCall(Env env, List<String> intronicCalls, List<String> exonicCalls, int idx) {
+
+    String intronicCall = ".";
+    if (intronicCalls.size() > idx) {
+      intronicCall = intronicCalls.get(idx);
+    }
+    String exonicCall = ".";
+    if (exonicCalls.size() > idx) {
+      exonicCall = exonicCalls.get(idx);
+    }
+
+    if (m_hapB3IntronCall == null) {
+      m_hapB3IntronCall = new ArrayList<>();
+    }
+    if (m_hapB3Call == null) {
+      m_hapB3Call = new ArrayList<>();
+    }
+
     // intronic call trumps exonic call
     if (intronicCall.equals("0")) {
       m_hapB3IntronCall.add("0");
@@ -154,7 +185,7 @@ private void handlePhasedCall(Env env, String intronicCall, String exonicCall) {
       if (!exonicCall.equals("0")) {
         m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
       }
-    } else {
+    } else if (intronicCall.equals("1")) {
       if (exonicCall.equals("0")) {
         m_hapB3IntronCall.add("1");
         m_hapB3Call.add("0");
@@ -162,6 +193,19 @@ private void handlePhasedCall(Env env, String intronicCall, String exonicCall) {
         m_hapB3IntronCall.add("0");
         m_hapB3Call.add("1");
       }
+    } else {
+      // intronic call is "."
+      m_hapB3IntronCall.add(".");
+      if (exonicCall.equals("1")) {
+        m_hapB3Call.add("1");
+      } else {
+        // if intronic is "0" or "."
+        m_hapB3Call.add(".");
+      }
+      if (!exonicCall.equals("0")) {
+        m_warning = env.getMessage(MessageHelper.MSG_DPYD_HAPB3_INTRONIC_MISMATCH_EXONIC);
+      }
+
     }
   }
 
@@ -171,14 +215,25 @@ private void handlePhasedCall(Env env, String intronicCall, String exonicCall) {
   private List<String> callHapB3(NamedAllele hapB3Allele, VariantLocus locus, SampleAllele sampleAllele) {
     List<String> rez = new ArrayList<>();
     String exonAllele = Objects.requireNonNull(hapB3Allele.getAllele(locus));
-    rez.add(exonAllele.equals(sampleAllele.getAllele1()) ? "1" : "0");
+    int count = 0;
+    if (sampleAllele.getAllele1() == null) {
+      if (sampleAllele.isPhased()) {
+        // we only care if this is phased
+        rez.add(".");
+      }
+    } else {
+      rez.add(exonAllele.equals(sampleAllele.getAllele1()) ? "1" : "0");
+      count += 1;
+    }
     if (sampleAllele.getAllele2() != null) {
       rez.add(exonAllele.equals(sampleAllele.getAllele2()) ? "1" : "0");
-    } else {
+      count += 1;
+    }
+    if (count < 2) {
       // this warning can get overwritten!
       // but we don't really care
       m_warning = new MessageAnnotation(MessageAnnotation.TYPE_NOTE, "warn.alleleCount",
-          "Only found 1 allele for " + locus.getRsid());
+          "Only found " + count + " allele for " + locus.getRsid());
     }
     return rez;
   }
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java
index 1a23ae85..7de3da32 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java
@@ -1,17 +1,7 @@
 package org.pharmgkb.pharmcat.haplotype;
 
 import java.lang.invoke.MethodHandles;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.stream.Collectors;
 import com.google.common.base.Preconditions;
 import com.google.gson.annotations.Expose;
@@ -114,7 +104,7 @@ public MatchData(String sampleId, String gene, SortedMap<String, SampleAllele> a
         }
       }
     }
-    m_isHaploid = m_sampleMap.values().stream().allMatch(sa -> sa.getAllele2() == null);
+    m_isHaploid = areSampleAllelesHaploid(m_sampleMap.values());
     m_isPhased = m_sampleMap.values().stream().allMatch(SampleAllele::isPhased);
     m_isHomozygous = m_isHaploid ||
         m_sampleMap.values().stream().allMatch(SampleAllele::isHomozygous);
@@ -376,4 +366,19 @@ protected SortedSet<HaplotypeMatch> comparePermutations() {
   public String toString() {
     return m_gene + " match data for " + m_sampleId;
   }
+
+
+  private static boolean areSampleAllelesHaploid(Collection<SampleAllele> sampleAlleles) {
+    int s1 = 0;
+    int s2 = 0;
+    for (SampleAllele a : sampleAlleles) {
+      if (a.getAllele1() == null) {
+        s1 += 1;
+      }
+      if (a.getAllele2() == null) {
+        s2 += 1;
+      }
+    }
+    return s1 == sampleAlleles.size() || s2 == sampleAlleles.size();
+  }
 }
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/SampleAllele.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/SampleAllele.java
index fe16a232..7ecd9d6d 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/SampleAllele.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/SampleAllele.java
@@ -47,6 +47,12 @@ public class SampleAllele implements Comparable<SampleAllele> {
   @SerializedName("vcfAlleles")
   private final List<String> m_vcfAlleles;
   @Expose
+  @SerializedName("gt")
+  private final String m_gt;
+  @Expose
+  @SerializedName("vcfCall")
+  private final String m_vcfCall;
+  @Expose
   @SerializedName("undocumentedVariations")
   private final Set<String> m_undocumentedVariations = new HashSet<>();
   @Expose
@@ -54,8 +60,8 @@ public class SampleAllele implements Comparable<SampleAllele> {
   private boolean m_treatUndocumentedVariationsAsReference;
 
 
-  public SampleAllele(String chromosome, long position, String a1, @Nullable String a2, boolean isPhased,
-      boolean isEffectivelyPhased, List<String> vcfAlleles, @Nullable Set<String> undocumentedVariations,
+  public SampleAllele(String chromosome, long position, @Nullable String a1, @Nullable String a2, boolean isPhased,
+      boolean isEffectivelyPhased, List<String> vcfAlleles, String gt, @Nullable Set<String> undocumentedVariations,
       boolean treatUndocumentedAsReference) {
     Preconditions.checkNotNull(vcfAlleles);
     m_chromosome = chromosome;
@@ -66,16 +72,32 @@ public SampleAllele(String chromosome, long position, String a1, @Nullable Strin
       m_undocumentedVariations.addAll(undocumentedVariations);
     }
     m_vcfAlleles = vcfAlleles;
+    m_gt = gt;
 
-    m_allele1 = a1.toUpperCase();
-    m_computedAllele1 = computeAllele(m_allele1, treatUndocumentedAsReference);
+    StringBuilder callBuilder = new StringBuilder();
+    if (a1 != null) {
+      m_allele1 = a1.toUpperCase();
+      m_computedAllele1 = computeAllele(m_allele1, treatUndocumentedAsReference);
+      callBuilder.append(m_allele1);
+    } else {
+      m_allele1 = null;
+      m_computedAllele1 = null;
+      callBuilder.append(".");
+    }
     if (a2 != null) {
       m_allele2 = a2.toUpperCase();
       m_computedAllele2 = computeAllele(m_allele2, treatUndocumentedAsReference);
+      if (isPhased) {
+        callBuilder.append("|");
+      } else {
+        callBuilder.append("/");
+      }
+      callBuilder.append(m_allele2);
     } else {
       m_allele2 = null;
       m_computedAllele2 = null;
     }
+    m_vcfCall = callBuilder.toString();
     m_isPhased = isPhased;
     m_isEffectivelyPhased = isEffectivelyPhased;
   }
@@ -89,11 +111,11 @@ private String computeAllele(String allele, boolean treatUndocumentedAsReference
   }
 
   /**
-   * This constructor is primarily for use in tests only.
+   * This constructor should only be use in tests.
    */
-  protected SampleAllele(String chromosome, long position, String a1, @Nullable String a2,
-      boolean isPhased, List<String> vcfAlleles) {
-    this(chromosome, position, a1, a2, isPhased, isPhased, vcfAlleles, null, false);
+  protected SampleAllele(String chromosome, long position, @Nullable String a1, @Nullable String a2,
+      boolean isPhased, List<String> vcfAlleles, String gt) {
+    this(chromosome, position, a1, a2, isPhased, isPhased, vcfAlleles, gt, null, false);
   }
 
 
@@ -112,7 +134,7 @@ public String getChrPosition() {
   /**
    * Gets the first allele from the VCF (per GT column).
    */
-  public String getAllele1() {
+  public @Nullable String getAllele1() {
     return m_allele1;
   }
 
@@ -127,7 +149,7 @@ public String getAllele1() {
   /**
    * Gets the first allele, taking treatUndocumentedVariationsAsReference into account.
    */
-  public String getComputedAllele1() {
+  public @Nullable String getComputedAllele1() {
     return m_computedAllele1;
   }
 
@@ -160,8 +182,27 @@ public List<String> getVcfAlleles() {
     return m_vcfAlleles;
   }
 
+  /**
+   * Gets the GT value from the VCF.
+   */
+  public String getGt() {
+    return m_gt;
+  }
+
+  /**
+   * Gets the alleles separated by VCF phasing delimiter (i.e. "/" or "|").
+   * Missing allele will be represented by ".".
+   */
+  public String getVcfCall() {
+    return m_vcfCall;
+  }
 
   public boolean isHomozygous() {
+    if (m_computedAllele1 == null) {
+      // both alleles can never be null
+      Preconditions.checkState(m_computedAllele2 != null);
+      return false;
+    }
     return m_computedAllele1.equals(m_computedAllele2);
   }
 
@@ -180,7 +221,7 @@ public boolean isTreatUndocumentedVariationsAsReference() {
 
   @Override
   public String toString() {
-    return m_allele1 + (m_allele2 == null ? "" : "/" + m_allele2) + " @ " + m_chromosome + ":" + m_position;
+    return m_vcfCall + " @ " + m_chromosome + ":" + m_position;
   }
 
   @Override
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java
index 3ab35540..afbb37c7 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java
@@ -19,6 +19,7 @@
 import java.util.zip.GZIPInputStream;
 import com.google.common.base.Preconditions;
 import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.SortedSetMultimap;
 import com.google.common.collect.TreeMultimap;
 import org.checkerframework.checker.nullness.qual.Nullable;
@@ -31,6 +32,7 @@
 import org.pharmgkb.parser.vcf.model.VcfMetadata;
 import org.pharmgkb.parser.vcf.model.VcfPosition;
 import org.pharmgkb.parser.vcf.model.VcfSample;
+import org.pharmgkb.pharmcat.ParseException;
 import org.pharmgkb.pharmcat.VcfFile;
 import org.pharmgkb.pharmcat.definition.DefinitionReader;
 import org.pharmgkb.pharmcat.definition.model.VariantLocus;
@@ -49,8 +51,8 @@
 public class VcfReader implements VcfLineParser {
   public static final String MSG_AD_FORMAT_MISSING = "AD format is not defined.  Assuming AD field is valid.";
   private static final Logger sf_logger = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+  private static final Set<String> sf_haploidChromosomes = ImmutableSet.of("chrY", "chrM");
   private static final Pattern sf_gtDelimiter = Pattern.compile("[|/]");
-  private static final Pattern sf_noCallPattern = Pattern.compile("^[.|/]+$");
   private static final Pattern sf_allelePattern = Pattern.compile("^[AaCcGgTt]+$");
   private static final String sf_filterCodeRef = "PCATxREF";
   private static final String sf_filterCodeAlt = "PCATxALT";
@@ -75,9 +77,11 @@ public class VcfReader implements VcfLineParser {
   /**
    * Constructor.
    * Reads in a VCF file and pulls the sample's alleles at positions of interest.
+   *
+   * @throws ParseException if there are no samples in the VCF file
    */
   public VcfReader(DefinitionReader definitionReader, BufferedReader vcfReader, @Nullable String sampleId,
-      boolean findCombinations) throws IOException {
+      boolean findCombinations) throws IOException, ParseException {
     m_locationsOfInterest = definitionReader.getLocationsOfInterest();
     m_locationsByGene = definitionReader.getLocationsByGene();
     m_sampleId = sampleId;
@@ -90,6 +94,8 @@ public VcfReader(DefinitionReader definitionReader, BufferedReader vcfReader, @N
   /**
    * Constructor.  Primarily used for testing.
    * This will read in the VCF file and pull the (first) sample's alleles at positions of interest.
+   *
+   * @throws ParseException if there are no samples in the VCF file
    */
   public VcfReader(DefinitionReader definitionReader, Path vcfFile) throws IOException {
     m_locationsOfInterest = definitionReader.getLocationsOfInterest();
@@ -103,6 +109,8 @@ public VcfReader(DefinitionReader definitionReader, Path vcfFile) throws IOExcep
   /**
    * Constructor.  Primarily for testing.
    * This will read in the VCF file and pull the sample's alleles at <em>ALL</em> positions.
+   *
+   * @throws ParseException if there are no samples in the VCF file
    */
   VcfReader(Path vcfFile) throws IOException {
     m_locationsOfInterest = null;
@@ -153,8 +161,10 @@ public SortedSetMultimap<String, String> getWarnings() {
 
   /**
    * Reads the VCF file.
+   *
+   * @throws ParseException if there are no samples in the VCF file
    */
-  private void read(Path vcfFile) throws IOException {
+  private void read(Path vcfFile) throws IOException, ParseException {
     Preconditions.checkNotNull(vcfFile);
     Preconditions.checkArgument(VcfFile.isVcfFile(vcfFile), "%s is not a VCF file", vcfFile);
 
@@ -165,8 +175,10 @@ private void read(Path vcfFile) throws IOException {
 
   /**
    * Read VCF data via reader.
+   *
+   * @throws ParseException if there are no samples in the VCF file
    */
-  private void read(BufferedReader reader) throws IOException {
+  private void read(BufferedReader reader) throws IOException, ParseException {
     // read VCF
     try (VcfParser vcfParser = new VcfParser.Builder()
         .fromReader(reader)
@@ -221,29 +233,32 @@ private void addWarning(String chrPos, String msg) {
   private void addWarning(String chrPos, String reportMsg, String clMsg) {
     // saved to report
     m_warnings.put(chrPos, reportMsg);
-    // prints to command line
+    // prints to the command line
     sf_logger.warn(clMsg);
   }
 
 
+  /**
+   * Parses a single line from VCF.
+   *
+   * @throws ParseException if there are no samples in the VCF file
+   */
   @Override
-  public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample> sampleData) {
-
-    final String chrPos = position.getChromosome() + ":" + position.getPosition();
+  public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample> sampleData) throws ParseException {
 
     if (sampleData.isEmpty()) {
-      sf_logger.warn("Missing sample data on {}", chrPos);
-      return;
+      throw new ParseException("VCF does not contain sample data");
     }
+
+    final String chrPos = position.getChromosome() + ":" + position.getPosition();
     if (m_alleleMap.containsKey(chrPos)) {
       addWarning(chrPos, "Duplicate entry found in VCF; this entry trumps others.",
           "Duplicate entry: first valid position wins");
       return;
     }
 
-    String gt = sampleData.get(m_sampleIdx).getProperty("GT");
-    VariantLocus varLoc;
-    Set<String> undocumentedVariations = new HashSet<>();
+    // only care about locations of interest
+    VariantLocus varLoc = null;
     if (m_locationsOfInterest != null) {
       varLoc = m_locationsOfInterest.get(chrPos);
       if (varLoc == null) {
@@ -259,15 +274,68 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
         addWarning(chrPos, "PharmCAT preprocessor detected REF mismatch (filter " + sf_filterCodeRef +
             ") but this does not match current data.  Was the VCF preprocessed with a different version of PharmCAT?");
       }
+    } else {
+      // for some reason we don't have locations of interest, so pass on warnings from preprocessor
+      if (position.getFilters().contains(sf_filterCodeRef)) {
+        addWarning(chrPos, "Discarded genotype at this position because REF in VCF (" + position.getRef() +
+            ") does not match expected reference");
+        m_discardedPositions.add(chrPos);
+        return;
+      }
+      if (position.getFilters().contains(sf_filterCodeAlt)) {
+        addWarning(chrPos, "The genetic variation at this position does not match what is in the allele definition");
+      }
+      if (position.getFilters().contains(sf_filterCodeIndel)) {
+        addWarning(chrPos, "Genotype at this position uses unexpected format for INDEL");
+      }
+    }
+
+
+    String gt = sampleData.get(m_sampleIdx).getProperty("GT");
+    if (gt == null) {
+      addWarning(chrPos, "Ignoring: no genotype");
+      m_discardedPositions.add(chrPos);
+      return;
+    }
+    String[] gtArray = sf_gtDelimiter.split(gt);
+    List<Integer> gtNonMissing = Arrays.stream(gtArray)
+        .filter(g -> !g.equals("."))
+        .map(Integer::parseInt)
+        .toList();
+    if (gtNonMissing.isEmpty()) {
+      addWarning(chrPos, "Ignoring: no call (" + gt + ")");
+      m_discardedPositions.add(chrPos);
+      return;
+    }
 
-      Set<Integer> gtCalls = new HashSet<>();
-      if (gt != null && !sf_noCallPattern.matcher(gt).matches()) {
-        Arrays.stream(sf_gtDelimiter.split(gt))
-            .filter(a -> !a.equals("."))
-            .map(Integer::parseInt)
-            .forEach(gtCalls::add);
+    if (sf_haploidChromosomes.contains(position.getChromosome())) {
+      // expect a single allele
+      if (gtNonMissing.size() > 1) {
+        addWarning(chrPos, gtNonMissing.size() + " genotypes found (" + getGeneForWarning(chrPos) +
+            ") for haploid chromosome. Will only use first non-missing genotype.");
       }
+    } else {
+      // diploid chromosome
+      if (gtNonMissing.size() > 2) {
+        addWarning(chrPos, gtNonMissing.size() + " genotypes found" + getGeneForWarning(chrPos) +
+            ". Will only use first two genotypes.");
+      } else if (gtNonMissing.size() == 1) {
+        if (!position.getChromosome().equals("chrX")) {
+          if (gtNonMissing.get(0) == 0) {
+            // treating "./0" like any other missing position
+            addWarning(chrPos, "Ignoring: only a single genotype found (GT=" + gt +
+                ").  Since it's reference, treating this as a missing position.");
+            m_discardedPositions.add(chrPos);
+            return;
+          }
+          addWarning(chrPos, gtNonMissing.size() + " genotype found" + getGeneForWarning(chrPos) + ", expecting 2.");
+        }
+      }
+    }
 
+    Set<String> undocumentedVariations = new HashSet<>();
+    Set<Integer> gtUnique = new HashSet<>(gtNonMissing);
+    if (varLoc != null) {
       // strip out structural alts (e.g. <*>)
       List<String> altBases = position.getAltBases().stream()
           .filter(a -> !a.startsWith("<"))
@@ -285,7 +353,7 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
         }
       } else {
         for (int x = 0; x < altBases.size(); x += 1) {
-          if (gtCalls.contains(x + 1)) {
+          if (gtUnique.contains(x + 1)) {
             String alt = altBases.get(x);
             if (!varLoc.getAlts().contains(alt)) {
               undocumentedVariations.add(alt);
@@ -311,45 +379,15 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
               ").  Was the VCF preprocessed with a different version of PharmCAT?");
         }
       }
-
-    } else {
-      // for some reason we don't have locations of interest, so pass on warnings from preprocessor
-      if (position.getFilters().contains(sf_filterCodeRef)) {
-        addWarning(chrPos, "Discarded genotype at this position because REF in VCF (" + position.getRef() +
-            ") does not match expected reference");
-        m_discardedPositions.add(chrPos);
-        return;
-      }
-      if (position.getFilters().contains(sf_filterCodeAlt)) {
-        addWarning(chrPos, "The genetic variation at this position does not match what is in the allele definition");
-      }
-      if (position.getFilters().contains(sf_filterCodeIndel)) {
-        addWarning(chrPos, "Genotype at this position uses unexpected format for INDEL");
-      }
     }
 
     if (sampleData.size() > 1 && !m_useSpecificSample) {
-      addWarning(chrPos, "Multiple samples found, only using first entry.");
+      // only warn once
+      if (m_alleleMap.isEmpty()) {
+        addWarning(chrPos, "Multiple samples found, only using first entry.");
+      }
     }
 
-    if (gt == null) {
-      addWarning(chrPos, "Ignoring: no genotype");
-      m_discardedPositions.add(chrPos);
-      return;
-    }
-    if (sf_noCallPattern.matcher(gt).matches()) {
-      addWarning(chrPos, "Ignoring: no call (" + gt + ")");
-      m_discardedPositions.add(chrPos);
-      return;
-    }
-    // already filtered out no-calls, guaranteed to have at least 1 GT here
-    String[] gtArray = sf_gtDelimiter.split(gt);
-    int[] alleleIndices = Arrays.stream(gtArray)
-        .filter(a -> !a.equals("."))
-        .mapToInt(Integer::parseInt)
-        .toArray();
-    boolean isHaploid = gtArray.length == 1;
-
     // normalize alleles to use the same syntax as haplotype definition
     List<String> alleles = new ArrayList<>();
     if (position.getAltBases().isEmpty()) {
@@ -364,10 +402,9 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
 
     } else {
       String gt1 = position.getAllele(0);
-      List<Integer> selected = Arrays.stream(alleleIndices).boxed().toList();
       for (int x = 1; x <= position.getAltBases().size(); x += 1) {
         String gt2 = position.getAllele(x);
-        boolean isSelected = selected.contains(x);
+        boolean isSelected = gtNonMissing.contains(x);
         if (!validateAlleles(chrPos, gt1, gt2, isSelected)) {
           m_discardedPositions.add(chrPos);
           return;
@@ -406,8 +443,7 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
                 .map(Integer::parseInt)
                 .toList();
             Map<Integer, Integer> genotype = new HashMap<>();
-            Arrays.stream(alleleIndices)
-                .forEach(g -> genotype.merge(g, 1, Integer::sum));
+            gtNonMissing.forEach(g -> genotype.merge(g, 1, Integer::sum));
             // GT is het, but AD is not (only one side has any reads)
             if (genotype.size() != 1 && depths.stream().filter(d -> d > 0).count() == 1) {
               addWarning(chrPos, "Discarding genotype at this position because GT field indicates heterozygous (" +
@@ -422,32 +458,20 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
       }
     }
 
-    for (int alleleIdx : alleleIndices) {
+    for (int alleleIdx : gtNonMissing) {
       if (alleleIdx >= alleles.size()) {
         throw new VcfFormatException("Invalid GT allele value (" + alleleIdx + ") for " + chrPos +
             " (only " + (alleles.size() - 1) + " ALT allele" + (alleles.size() > 1 ? "s" : "") + " specified)");
       }
     }
 
-    String a1 = alleles.get(alleleIndices[0]);
-    String a2 = isHaploid ? null : ".";
-    if (alleleIndices.length > 1) {
-      a2 = alleles.get(alleleIndices[1]);
-      if (alleleIndices.length > 2) {
-        addWarning(chrPos, alleleIndices.length + " genotypes found.  Only using first 2 genotypes.");
-      }
-    } else if (!position.getChromosome().equals("chrM") &&
-        !position.getChromosome().equals("chrY") &&
-        !position.getChromosome().equals("chrX")) {
-      if (alleleIndices[0] == 0) {
-        // treating "./0" like any other missing position
-        addWarning(chrPos, "Ignoring: only a single genotype found.  " +
-            "Since it's reference, treating this as a missing position.");
-        m_discardedPositions.add(chrPos);
-        return;
-      }
-      // going to accept "./1" because there's a variation, and we want to pass this on to the reporter
-      addWarning(chrPos, "Only a single genotype found.");
+    String a1 = null;
+    if (!gtArray[0].equals(".")) {
+      a1 = alleles.get(Integer.parseInt(gtArray[0]));
+    }
+    String a2 = null;
+    if (gtArray.length > 1 && !gtArray[1].equals(".")) {
+      a2 = alleles.get(Integer.parseInt(gtArray[1]));
     }
 
     // genotype divided by "|" if phased and "/" if unphased
@@ -455,9 +479,9 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
     boolean isEffectivelyPhased = true;
     if (gt.contains("/")) {
       isPhased = false;
-      // we'll also treat homozygous as phased
-       if (a2 != null && !a1.equalsIgnoreCase(a2)) {
-         isEffectivelyPhased = false;
+      if (gtUnique.size() > 1) {
+        // we'll also treat homozygous as phased
+        isEffectivelyPhased = false;
        }
     }
 
@@ -467,7 +491,7 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
 
     boolean treatUndocumentedAsReference = m_locationsByGene != null && treatUndocumentedAsReference(chrPos);
     SampleAllele sampleAllele = new SampleAllele(position.getChromosome(), position.getPosition(), a1, a2, isPhased,
-        isEffectivelyPhased, vcfAlleles, undocumentedVariations, treatUndocumentedAsReference);
+        isEffectivelyPhased, vcfAlleles, gt, undocumentedVariations, treatUndocumentedAsReference);
     m_alleleMap.put(chrPos, sampleAllele);
     if (m_discardedPositions.contains(chrPos)) {
       addWarning(chrPos, "Duplicate entry found in VCF; this entry trumps previous invalid entry.",
@@ -475,6 +499,17 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
     }
   }
 
+  /**
+   * Gets gene {@code chrPos} is in surrounded by parentheses for use in warnings.
+   * <p>
+   * Example: {@code " (TPMT)"}
+   */
+  private String getGeneForWarning(String chrPos) {
+    if (m_locationsByGene == null) {
+      return "";
+    }
+    return " (" + m_locationsByGene.get(chrPos) + ")";
+  }
 
   private boolean treatUndocumentedAsReference(String chrPos) {
     String gene = m_locationsByGene.get(chrPos);
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/model/Variant.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/model/Variant.java
index 2378abf6..be0f1863 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/model/Variant.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/model/Variant.java
@@ -35,30 +35,19 @@ public class Variant implements Comparable<Variant>  {
    */
   public Variant(VariantLocus variant, SampleAllele allele) {
     String vcfAlleles = sf_vcfAlleleJoiner.join(allele.getVcfAlleles());
-
-    StringBuilder callBuilder = new StringBuilder()
-        .append(allele.getAllele1());
-    if (allele.getAllele2() != null) {
-      if (allele.isPhased()) {
-        callBuilder.append("|");
-      } else {
-        callBuilder.append("/");
-      }
-      callBuilder.append(allele.getAllele2());
-    }
-    initialize(variant.getPosition(), variant.getRsid(), callBuilder.toString(), vcfAlleles);
+    initialize(variant.getPosition(), variant.getRsid(), allele.getVcfCall(), vcfAlleles);
   }
 
   /**
    * Constructor for creating faux-{@link Variant}s for extra positions and tests.
    */
-  public Variant(long pos, @Nullable String rsids, @Nullable String call, @Nullable String vcfAlleles) {
-    initialize(pos, rsids, call, vcfAlleles);
+  public Variant(long pos, @Nullable String rsid, @Nullable String call, @Nullable String vcfAlleles) {
+    initialize(pos, rsid, call, vcfAlleles);
   }
 
-  private void initialize(long pos, @Nullable String rsids, @Nullable String call, @Nullable String vcfAlleles) {
+  private void initialize(long pos, @Nullable String rsid, @Nullable String call, @Nullable String vcfAlleles) {
     m_position = pos;
-    m_rsid = rsids;
+    m_rsid = rsid;
     m_vcfCall = call;
     if (call != null) {
       // check for phasing by lack of "/" to match behavior in VCF reader
@@ -76,6 +65,10 @@ public long getPosition() {
     return m_rsid;
   }
 
+  /**
+   * Gets the alleles separated by VCF phasing delimiter (i.e. "/" or "|").
+   * Missing allele will be represented by ".".
+   */
   public @Nullable String getVcfCall() {
     return m_vcfCall;
   }
@@ -84,6 +77,9 @@ public boolean isPhased() {
     return m_isPhased;
   }
 
+  /**
+   * Gets the comma-separated list of all possible alleles from the VCF (i.e. REF and ALT).
+   */
   public @Nullable String getVcfAlleles() {
     return m_vcfAlleles;
   }
diff --git a/src/test/java/org/pharmgkb/pharmcat/DpydTest.java b/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
index 67cc91a4..17619fc2 100644
--- a/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
+++ b/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
@@ -47,12 +47,12 @@ class DpydTest {
   @BeforeAll
   static void prepare() {
     ReportHelpers.setDebugMode(true);
-    //TestUtils.setSaveTestOutput(true);
+    TestUtils.setSaveTestOutput(true);
   }
 
   @AfterEach
   void deleteDirectory(TestInfo testInfo) {
-    TestUtils.deleteTestOutputDirectory(testInfo);
+    //TestUtils.deleteTestOutputDirectory(testInfo);
   }
 
 
@@ -253,9 +253,10 @@ static void dpydHtmlChecks(Document document, @Nullable List<String> expectedCal
       assertEquals(1, capecitabineSection.size());
       Elements missingVariantsWarning = capecitabineSection.get(0).select(".alert-info.missing-variants");
       if (hasMissingPositions) {
-        assertEquals(1, missingVariantsWarning.size());
+        assertEquals(1, missingVariantsWarning.size(), "Expected missing variants, but found none");
       } else {
-        assertEquals(0, missingVariantsWarning.size());
+        assertEquals(0, missingVariantsWarning.size(), "Expected no missing variants, but found " +
+            missingVariantsWarning.size());
       }
 
       List<String> expectedRxCalls = cpicStyleCalls == null ?
@@ -771,6 +772,40 @@ void hapB3AndIntronicC(TestInfo testInfo) throws Exception {
     dpydHtmlChecks(document, expectedCalls, false, hasDpwgAnnotations);
   }
 
+  @Test
+  void hapB3AndIntronicC_missingFirstAllele(TestInfo testInfo) throws Exception {
+
+    PipelineWrapper testWrapper = new PipelineWrapper(testInfo, true, false, false)
+        .saveIntermediateFiles();
+    testWrapper.getVcfBuilder()
+        .phased()
+        // hapB3 exon C>T
+        .variation("DPYD", "rs56038477", ".", "T")
+        // hapB3 intron G>C
+        .variation("DPYD", "rs75017182", ".", "C")
+    ;
+
+    Path vcfFile = testWrapper.execute();
+
+    List<String> expectedCalls = List.of(
+        "Reference/c.1129-5923C>G, c.1236G>A (HapB3)"
+    );
+    List<String> cpicStyleCalls = List.of(
+        "c.1129-5923C>G, c.1236G>A (HapB3) (heterozygous)"
+    );
+    RecPresence hasDpwgAnnotations = RecPresence.YES;
+
+    testWrapper.testCalledByMatcher("DPYD");
+    testWrapper.testSourceDiplotypes(DataSource.CPIC, "DPYD", expectedCalls, cpicStyleCalls);
+    testWrapper.testRecommendedDiplotypes(DataSource.CPIC, "DPYD", List.of("Reference", DpydHapB3Matcher.HAPB3_ALLELE));
+    testWrapper.testPrintCalls(DataSource.CPIC, "DPYD", cpicStyleCalls);
+
+    dpydHasReports(testWrapper, hasDpwgAnnotations);
+
+    Document document = readHtmlReport(vcfFile);
+    dpydHtmlChecks(document, expectedCalls, cpicStyleCalls, true, RecPresence.YES, hasDpwgAnnotations);
+  }
+
   @Test
   void hapB3AndIntronicD(TestInfo testInfo) throws Exception {
 
diff --git a/src/test/java/org/pharmgkb/pharmcat/TestVcfBuilder.java b/src/test/java/org/pharmgkb/pharmcat/TestVcfBuilder.java
index 49d0ce31..bb249854 100644
--- a/src/test/java/org/pharmgkb/pharmcat/TestVcfBuilder.java
+++ b/src/test/java/org/pharmgkb/pharmcat/TestVcfBuilder.java
@@ -10,7 +10,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.junit.jupiter.api.TestInfo;
 import org.pharmgkb.pharmcat.definition.DefinitionReader;
@@ -343,7 +342,9 @@ private void handleCustomEdit(DefinitionFile definitionFile, PrintWriter writer,
       }
       String vcfAllele = vl.getCpicToVcfAlleleMap().get(cpicAllele);
       if (vcfAllele == null) {
-        if (m_allowUnknownAllele) {
+        if (cpicAllele.equals(".")) {
+          vcfAllele = ".";
+        } else if (m_allowUnknownAllele) {
           vcfAllele = cpicAllele;
           alts.add(vcfAllele);
         } else {
@@ -351,7 +352,9 @@ private void handleCustomEdit(DefinitionFile definitionFile, PrintWriter writer,
               ", expected one of " + vl.getCpicToVcfAlleleMap().keySet());
         }
       }
-      if (vcfAllele.equals(vl.getRef())) {
+      if (vcfAllele.equals(".")) {
+        builder.append(".");
+      } else if (vcfAllele.equals(vl.getRef())) {
         builder.append("0");
       } else {
         int idx = alts.indexOf(vcfAllele);
diff --git a/src/test/java/org/pharmgkb/pharmcat/haplotype/CombinationUtilTest.java b/src/test/java/org/pharmgkb/pharmcat/haplotype/CombinationUtilTest.java
index 79691c87..2ff974c7 100644
--- a/src/test/java/org/pharmgkb/pharmcat/haplotype/CombinationUtilTest.java
+++ b/src/test/java/org/pharmgkb/pharmcat/haplotype/CombinationUtilTest.java
@@ -26,10 +26,10 @@ class CombinationUtilTest {
   void testGeneratePermutationsNotPhased() {
 
     List<SampleAllele> alleles = Arrays.asList(
-        new SampleAllele("chr1", 1, "T", "T", false, Lists.newArrayList("T", "C")),
-        new SampleAllele("chr1", 2, "A", "T", false, Lists.newArrayList("A", "T")),
-        new SampleAllele("chr1", 3, "C", "C", false, Lists.newArrayList("C", "C")),
-        new SampleAllele("chr1", 4, "C", "G", false, Lists.newArrayList("C", "G"))
+        new SampleAllele("chr1", 1, "T", "T", false, Lists.newArrayList("T", "C"), "0/0"),
+        new SampleAllele("chr1", 2, "A", "T", false, Lists.newArrayList("A", "T"),  "0/1"),
+        new SampleAllele("chr1", 3, "C", "C", false, Lists.newArrayList("C", "C"), "0/0"),
+        new SampleAllele("chr1", 4, "C", "G", false, Lists.newArrayList("C", "G"), "0/1")
     );
 
     Set<String> expectedPermutations = Sets.newHashSet(
@@ -49,10 +49,10 @@ void testGeneratePermutationsNotPhased() {
   void testGeneratePermutationPhased() {
 
     List<SampleAllele> alleles = Arrays.asList(
-        new SampleAllele("chr1", 1, "T", "T", true, Lists.newArrayList("T", "C")),
-        new SampleAllele("chr1", 2, "A", "T", true, Lists.newArrayList("A", "T")),
-        new SampleAllele("chr1", 3, "C", "C", true, Lists.newArrayList("C", "C")),
-        new SampleAllele("chr1", 4, "C", "G", true, Lists.newArrayList("C", "G"))
+        new SampleAllele("chr1", 1, "T", "T", true, Lists.newArrayList("T", "C"), "0|0"),
+        new SampleAllele("chr1", 2, "A", "T", true, Lists.newArrayList("A", "T"), "0|1"),
+        new SampleAllele("chr1", 3, "C", "C", true, Lists.newArrayList("C", "C"), "0|0"),
+        new SampleAllele("chr1", 4, "C", "G", true, Lists.newArrayList("C", "G"), "0|1")
     );
 
     Set<String> expectedPermutations = Sets.newHashSet(
diff --git a/src/test/java/org/pharmgkb/pharmcat/haplotype/DiplotypeMatcherTest.java b/src/test/java/org/pharmgkb/pharmcat/haplotype/DiplotypeMatcherTest.java
index 70752bce..e7e00e05 100644
--- a/src/test/java/org/pharmgkb/pharmcat/haplotype/DiplotypeMatcherTest.java
+++ b/src/test/java/org/pharmgkb/pharmcat/haplotype/DiplotypeMatcherTest.java
@@ -85,9 +85,9 @@ static void beforeClass() {
   void test1() {
 
     SortedSet<SampleAllele> alleles = new TreeSet<>(Arrays.asList(
-        new SampleAllele("chr1", 1, "A", "G", false, Lists.newArrayList("A", "G")),
-        new SampleAllele("chr1", 2, "C", "C", false, Lists.newArrayList("C", "T")),
-        new SampleAllele("chr1", 3, "C", "C", false, Lists.newArrayList("C", "T"))
+        new SampleAllele("chr1", 1, "A", "G", false, Lists.newArrayList("A", "G"), "0/1"),
+        new SampleAllele("chr1", 2, "C", "C", false, Lists.newArrayList("C", "T"), "0/0"),
+        new SampleAllele("chr1", 3, "C", "C", false, Lists.newArrayList("C", "T"), "0/0")
     ));
 
     SortedSet<DiplotypeMatch> pairMatches = computeHaplotypes(alleles);
@@ -100,9 +100,9 @@ void test1() {
   void test2() {
 
     SortedSet<SampleAllele> alleles = new TreeSet<>(Arrays.asList(
-        new SampleAllele("chr1", 1, "A", "G", false, Lists.newArrayList("A", "G")),
-        new SampleAllele("chr1", 2, "C", "T", false, Lists.newArrayList("C", "T")),
-        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"))
+        new SampleAllele("chr1", 1, "A", "G", false, Lists.newArrayList("A", "G"), "0/1"),
+        new SampleAllele("chr1", 2, "C", "T", false, Lists.newArrayList("C", "T"), "0/1"),
+        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"), "0/1")
     ));
 
     SortedSet<DiplotypeMatch> pairMatches = computeHaplotypes(alleles);
@@ -115,9 +115,9 @@ void test2() {
   void test3() {
 
     SortedSet<SampleAllele> alleles = new TreeSet<>(Arrays.asList(
-        new SampleAllele("chr1", 1, "A", "A", false, Lists.newArrayList("A", "G")),
-        new SampleAllele("chr1", 2, "C", "T", false, Lists.newArrayList("C", "T")),
-        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"))
+        new SampleAllele("chr1", 1, "A", "A", false, Lists.newArrayList("A", "G"), "0/0"),
+        new SampleAllele("chr1", 2, "C", "T", false, Lists.newArrayList("C", "T"), "0/1"),
+        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"), "0/1")
     ));
 
     SortedSet<DiplotypeMatch> pairMatches = computeHaplotypes(alleles);
@@ -130,9 +130,9 @@ void test3() {
   void test4() {
 
     SortedSet<SampleAllele> alleles = new TreeSet<>(Arrays.asList(
-        new SampleAllele("chr1", 1, "G", "G", false, Lists.newArrayList("A", "G")),
-        new SampleAllele("chr1", 2, "T", "T", false, Lists.newArrayList("C", "T")),
-        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"))
+        new SampleAllele("chr1", 1, "G", "G", false, Lists.newArrayList("A", "G"), "1/1"),
+        new SampleAllele("chr1", 2, "T", "T", false, Lists.newArrayList("C", "T"), "1/1"),
+        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"), "0/1")
     ));
 
     SortedSet<DiplotypeMatch> pairMatches = computeHaplotypes(alleles);
@@ -145,9 +145,9 @@ void test4() {
   void test5() {
 
     SortedSet<SampleAllele> alleles = new TreeSet<>(Arrays.asList(
-        new SampleAllele("chr1", 1, "G", "G", false, Lists.newArrayList("A", "G")),
-        new SampleAllele("chr1", 2, "C", "T", false, Lists.newArrayList("C", "T")),
-        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"))
+        new SampleAllele("chr1", 1, "G", "G", false, Lists.newArrayList("A", "G"), "1/1"),
+        new SampleAllele("chr1", 2, "C", "T", false, Lists.newArrayList("C", "T"), "0/1"),
+        new SampleAllele("chr1", 3, "C", "T", false, Lists.newArrayList("C", "T"), "0/1")
     ));
     SortedSet<DiplotypeMatch> pairMatches = computeHaplotypes(alleles);
     List<String> expectedMatches = Lists.newArrayList("*4a/*4b", "*4a/*17", "*4a/*4a");
@@ -216,10 +216,10 @@ void testComparePermutations() {
         "1:T;2:T;3:C;4:G;"
     );
     SortedMap<String, SampleAllele> sampleAlleleMap = new TreeMap<>();
-    sampleAlleleMap.put("chr1:1", new SampleAllele("chr1", 1, "T", "T", true, Lists.newArrayList("T")));
-    sampleAlleleMap.put("chr1:2", new SampleAllele("chr1", 2, "A", "T", false, Lists.newArrayList("T")));
-    sampleAlleleMap.put("chr1:3", new SampleAllele("chr1", 3, "C", "C", false, Lists.newArrayList("C")));
-    sampleAlleleMap.put("chr1:4", new SampleAllele("chr1", 4, "C", "G", false, Lists.newArrayList("C")));
+    sampleAlleleMap.put("chr1:1", new SampleAllele("chr1", 1, "T", "T", true, Lists.newArrayList("T"), "0/0"));
+    sampleAlleleMap.put("chr1:2", new SampleAllele("chr1", 2, "A", "T", false, Lists.newArrayList("T"), "1/0"));
+    sampleAlleleMap.put("chr1:3", new SampleAllele("chr1", 3, "C", "C", false, Lists.newArrayList("C"), "0/0"));
+    sampleAlleleMap.put("chr1:4", new SampleAllele("chr1", 4, "C", "G", false, Lists.newArrayList("C"), "0/1"));
 
     MatchData dataset = new MatchData("Sample_1", "GENE", sampleAlleleMap, variants, null, null);
     dataset.marshallHaplotypes("TEST", new TreeSet<>(Lists.newArrayList(hap1, hap2, hap3)), false);
diff --git a/src/test/java/org/pharmgkb/pharmcat/haplotype/SampleAlleleTest.java b/src/test/java/org/pharmgkb/pharmcat/haplotype/SampleAlleleTest.java
index dcc2c73a..1d61fbe0 100644
--- a/src/test/java/org/pharmgkb/pharmcat/haplotype/SampleAlleleTest.java
+++ b/src/test/java/org/pharmgkb/pharmcat/haplotype/SampleAlleleTest.java
@@ -18,12 +18,12 @@ class SampleAlleleTest {
   @Test
   void testCompare() {
 
-    SampleAllele sa1 = new SampleAllele("chr1", 1, "A", "A", true, Lists.newArrayList("A", "G"));
-    SampleAllele sa2 = new SampleAllele("chr1", 2, "A", "A", true, Lists.newArrayList("A", "G"));
-    SampleAllele sa3 = new SampleAllele("chr2", 1, "A", "A", true, Lists.newArrayList("A", "G"));
-    SampleAllele sa4 = new SampleAllele("chrX", 1, "A", "A", true, Lists.newArrayList("A", "G"));
-    SampleAllele sa5 = new SampleAllele("chrY", 1, "A", "A", true, Lists.newArrayList("A", "G"));
-    SampleAllele sa6 = new SampleAllele("chr11", 1, "A", "A", true, Lists.newArrayList("A", "G"));
+    SampleAllele sa1 = new SampleAllele("chr1", 1, "A", "A", true, Lists.newArrayList("A", "G"), "0/0");
+    SampleAllele sa2 = new SampleAllele("chr1", 2, "A", "A", true, Lists.newArrayList("A", "G"), "0/0");
+    SampleAllele sa3 = new SampleAllele("chr2", 1, "A", "A", true, Lists.newArrayList("A", "G"), "0/0");
+    SampleAllele sa4 = new SampleAllele("chrX", 1, "A", "A", true, Lists.newArrayList("A", "G"), "0/0");
+    SampleAllele sa5 = new SampleAllele("chrY", 1, "A", "A", true, Lists.newArrayList("A", "G"), "0/0");
+    SampleAllele sa6 = new SampleAllele("chr11", 1, "A", "A", true, Lists.newArrayList("A", "G"), "0/0");
 
     assertSame(Sets.newTreeSet(Sets.newHashSet(sa1, sa2)).first(), sa1);
     assertSame(Sets.newTreeSet(Sets.newHashSet(sa2, sa1)).first(), sa1);
diff --git a/src/test/java/org/pharmgkb/pharmcat/haplotype/VcfReaderTest.java b/src/test/java/org/pharmgkb/pharmcat/haplotype/VcfReaderTest.java
index fc33d1bc..ecbb1816 100644
--- a/src/test/java/org/pharmgkb/pharmcat/haplotype/VcfReaderTest.java
+++ b/src/test/java/org/pharmgkb/pharmcat/haplotype/VcfReaderTest.java
@@ -31,6 +31,47 @@ void testCompressed() throws Exception {
   }
 
 
+  @Test
+  void testAlleleOrder() throws Exception {
+    VcfReader reader = new VcfReader(PathUtils.getPathToResource("org/pharmgkb/pharmcat/haplotype/VcfReaderTest-alleleOrder.vcf"));
+    Map<String, SampleAllele> alleleMap = reader.getAlleleMap();
+
+    assertEquals(4, alleleMap.size());
+
+    reader.getWarnings().keySet()
+        .forEach(p -> {
+          System.out.println(p);
+          for (String warning : reader.getWarnings().get(p)) {
+            System.out.println(" * " + warning);
+          }
+        });
+
+    // .|1
+    String chrPos = "chr1:97079005";
+    assertTrue(reader.getWarnings().containsKey(chrPos));
+    assertEquals(1, reader.getWarnings().get(chrPos).size());
+    assertTrue(reader.getWarnings().get(chrPos).contains("1 genotype found, expecting 2."));
+    SampleAllele sa = alleleMap.get(chrPos);
+    assertNotNull(sa);
+    assertNull(sa.getAllele1());
+    assertEquals("T", sa.getAllele2());
+
+    // .|1
+    assertTrue(reader.getWarnings().containsKey("chr1:97079071"));
+    assertEquals(1, reader.getWarnings().get("chr1:97079071").size());
+    assertTrue(reader.getWarnings().get("chr1:97079071").contains("1 genotype found, expecting 2."));
+
+    // 0|.
+    assertTrue(reader.getWarnings().containsKey("chr1:97079076"));
+    assertEquals(1, reader.getWarnings().get("chr1:97079076").size());
+    assertTrue(reader.getWarnings().get("chr1:97079076").contains("Ignoring: only a single genotype found (GT=0|.).  Since it's reference, treating this as a missing position."));
+    // .|0
+    assertTrue(reader.getWarnings().containsKey("chr1:97079077"));
+    assertEquals(1, reader.getWarnings().get("chr1:97079077").size());
+    assertTrue(reader.getWarnings().get("chr1:97079077").contains("Ignoring: only a single genotype found (GT=.|0).  Since it's reference, treating this as a missing position."));
+  }
+
+
   @Test
   void testPhasing() throws Exception {