diff --git a/src/compare_vcfs.py b/src/compare_vcfs.py
index a64e19c..56b4068 100644
--- a/src/compare_vcfs.py
+++ b/src/compare_vcfs.py
@@ -110,6 +110,13 @@ def make_compatible_genotypes(ds1, ds2, acgt_alleles=False):
     3. `ds1` and `ds2` have the same number of variable sites.
     4. `ds1` and `ds2` have the same allele list at each site.
 
+    Assumptions:
+    1. Only ACGT alleles.
+    2. No mixed ploidy.
+
+    Additionally, if `actg_alleles` is set to True,
+    all allele lists in `ds1` and `ds2` are set to ACGT.
+
     :param xarray.Dataset ds1: sgkit-style dataset.
     :param xarray.Dataset ds2: sgkit-style dataset.
     :param bool acgt_alleles: All allele lists are set to ACGT (default = False).
@@ -123,6 +130,11 @@ def make_compatible_genotypes(ds1, ds2, acgt_alleles=False):
     ds2_idx = np.array(ds2_idx.flatten())
     assert len(ds1_idx) == len(ds2_idx) == len(common_site_idx)
 
+    if acgt_alleles:
+        remapped_ds1_alleles, remapped_ds1_genotypes = remap_genotypes(ds2, ds1, acgt_alleles=acgt_alleles)
+        assert remapped_ds1_alleles.shape == (len(common_site_idx), 4)
+        assert remapped_ds1_genotypes.shape == (len(common_site_idx), ds1.dims["samples"], ds1.dims["ploidy"])
+
     remapped_ds2_alleles, remapped_ds2_genotypes = remap_genotypes(ds1, ds2, acgt_alleles=acgt_alleles)
     assert remapped_ds2_alleles.shape == (len(common_site_idx), 4)
     assert remapped_ds2_genotypes.shape == (len(common_site_idx), ds2.dims["samples"], ds2.dims["ploidy"])
@@ -131,8 +143,12 @@ def make_compatible_genotypes(ds1, ds2, acgt_alleles=False):
     ds1_subset = ds1.copy(deep=True)    # TODO: Copying is expensive, another way?
     ds1_subset["variant_contig"] = ds1_subset["variant_contig"].isel(variants=ds1_idx)
     ds1_subset["variant_position"] = ds1_subset["variant_position"].isel(variants=ds1_idx)
-    ds1_subset["variant_allele"] = remapped_ds2_alleles
-    ds1_subset["call_genotype"] = ds1_subset["call_genotype"].isel(variants=ds1_idx)
+    if acgt_alleles:
+        ds1_subset["variant_allele"] = remapped_ds1_alleles
+        ds1_subset["call_genotype"] = remapped_ds1_genotypes
+    else:
+        ds1_subset["variant_allele"] = remapped_ds2_alleles
+        ds1_subset["call_genotype"] = ds1_subset["call_genotype"].isel(variants=ds1_idx)
     ds1_subset["call_genotype_mask"] = ds1_subset["call_genotype_mask"].isel(variants=ds1_idx)
 
     # Subset `ds2` to common sites