final List<Allele> A_G_ALT = Arrays.asList(Aref, G, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
<BUG>final Genotype gA_G_ALT = new GenotypeBuilder("A_G").PL(standardPLs).make();
</BUG>
final VariantContext vcA_G_ALT = new VariantContextBuilder(VCbase).alleles(A_G_ALT).genotypes(gA_G_ALT).make();
final List<Allele> A_C_G = Arrays.asList(Aref, C, G);
<BUG>final Genotype gA_C_G = new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30}).make();
</BUG>
final List<Allele> A_C_G_ALT = Arrays.asList(Aref, C, G, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
<BUG>final Genotype gA_C_G_ALT = new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30, 71, 72, 73, 74}).make();
</BUG>
final VariantContext vcA_C_G_ALT = new VariantContextBuilder(VCbase).alleles(A_C_G_ALT).genotypes(gA_C_G_ALT).make();

final List<Allele> A_G_ALT = Arrays.asList(Aref, G, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
final Genotype gA_G_ALT = new GenotypeBuilder("A_G").PL(standardPLs).alleles(noCalls).make();
final VariantContext vcA_G_ALT = new VariantContextBuilder(VCbase).alleles(A_G_ALT).genotypes(gA_G_ALT).make();
final List<Allele> A_C_G = Arrays.asList(Aref, C, G);
final Genotype gA_C_G = new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30}).alleles(noCalls).make();
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();
