diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
index 1bcbc50e3..9cb294497 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
@@ -175,4 +175,22 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
                 Arrays.asList("67657ee509665fd0d7a2c9024981ba92"));
         executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec);
     }
+
+    @Test
+    public void testSplitLeftAlignmentWithMultiallelicNoCallGenotypes() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " --variant:vcf " + privateTestDir + "multiallelic-nocall.vcf -L chr12:104350950-104350960 --no_cmdline_in_header -split",
+                1,
+                Arrays.asList("c7ce4310117f993593ce35f586451c53"));
+        executeTest("test splitting left alignment of multiple alleles with no-call genoptypes", spec);
+    }
+
+    @Test
+    public void testSplitLeftAlignmentWithMultiallelicBadAD() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " --variant:vcf " + privateTestDir + "multiallelic-nocall-badAD.vcf -L chr12:104350950-104350960 --no_cmdline_in_header -split",
+                1,
+                 IllegalStateException.class);
+        executeTest("test splitting left alignment of multiple alleles with bad AD", spec);
+    }
 }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
index d67dd6c01..ce40acebe 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
@@ -927,7 +927,7 @@ public class GATKVariantContextUtils {
                 final List<Allele> best = new LinkedList<>();
                 final Allele ref = allelesToUse.get(0);
                 for ( final Allele originalAllele : originalGT ) {
-                    best.add(allelesToUse.contains(originalAllele) ? originalAllele : ref);
+                    best.add((allelesToUse.contains(originalAllele) || originalAllele.isNoCall()) ? originalAllele : ref);
                 }
                 gb.alleles(best);
                 break;
@@ -1045,7 +1045,7 @@ public class GATKVariantContextUtils {
         else {
             final List<VariantContext> biallelics = new LinkedList<>();
 
-            // if any of the genotypes ar ehet-not-ref (i.e. 1/2), set all of them to no-call
+            // if any of the genotypes are het-not-ref (i.e. 1/2), set all of them to no-call
             final GenotypeAssignmentMethod genotypeAssignmentMethodUsed = hasHetNonRef(vc.getGenotypes()) ? GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS : genotypeAssignmentMethod;
 
             for ( final Allele alt : vc.getAlternateAlleles() ) {
@@ -1466,6 +1466,10 @@ public class GATKVariantContextUtils {
 
         int currentIndex = 0;
         for ( int i = alleleIndexesToUse.nextSetBit(0); i >= 0; i = alleleIndexesToUse.nextSetBit(i+1) ) {
+            if ( i >= oldAD.length ) {
+                throw new IllegalStateException("AD has " + oldAD.length + " items. It should have at least " + (i+1) + ".");
+            }
+
             newAD[currentIndex++] = oldAD[i];
         }