</BUG>
final VariantContext vcA_ATC_ALT = new VariantContextBuilder(VCbase).alleles(A_ATC_ALT).genotypes(gA_ATC_ALT).make();
final Allele A = Allele.create("A", false);
final List<Allele> AA_A_ALT = Arrays.asList(AAref, A, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
<BUG>final Genotype gAA_A_ALT = new GenotypeBuilder("AA_A").PL(standardPLs).make();
</BUG>
final VariantContext vcAA_A_ALT = new VariantContextBuilder(VCprevBase).alleles(AA_A_ALT).genotypes(gAA_A_ALT).make();
tests.add(new Object[]{Arrays.asList(vcA_C_ALT),
loc, false,
<BUG>new VariantContextBuilder(VCbase).alleles(A_C).genotypes(gA_C).make()});
</BUG>
tests.add(new Object[]{Arrays.asList(vcA_C_ALT, vcA_G_ALT),

final List<Allele> A_C_G_ALT = Arrays.asList(Aref, C, G, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
final Genotype gA_C_G_ALT = new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30, 71, 72, 73, 74}).alleles(noCalls).make();
final VariantContext vcA_C_G_ALT = new VariantContextBuilder(VCbase).alleles(A_C_G_ALT).genotypes(gA_C_G_ALT).make();
final List<Allele> A_ATC_ALT = Arrays.asList(Aref, ATC, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
final Genotype gA_ATC_ALT = new GenotypeBuilder("A_ATC").PL(standardPLs).alleles(noCalls).make();
final VariantContext vcA_ATC_ALT = new VariantContextBuilder(VCbase).alleles(A_ATC_ALT).genotypes(gA_ATC_ALT).make();
final Allele A = Allele.create("A", false);
final List<Allele> AA_A_ALT = Arrays.asList(AAref, A, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
final Genotype gAA_A_ALT = new GenotypeBuilder("AA_A").PL(standardPLs).alleles(noCalls).make();
final VariantContext vcAA_A_ALT = new VariantContextBuilder(VCprevBase).alleles(AA_A_ALT).genotypes(gAA_A_ALT).make();
tests.add(new Object[]{Arrays.asList(vcA_C_ALT),
