diff --git a/src/compare_vcfs.py b/src/compare_vcfs.py
index 049a8e0..a64e19c 100644
--- a/src/compare_vcfs.py
+++ b/src/compare_vcfs.py
@@ -140,7 +140,7 @@ def make_compatible_genotypes(ds1, ds2, acgt_alleles=False):
     ds2_subset["variant_contig"] = ds2_subset["variant_contig"].isel(variants=ds2_idx)
     ds2_subset["variant_position"] = ds2_subset["variant_position"].isel(variants=ds2_idx)
     ds2_subset["variant_allele"] = remapped_ds2_alleles
-    ds2_subset["call_genotype"] = remapped_ds2_genotypes.isel(variants=ds2_idx)
+    ds2_subset["call_genotype"] = remapped_ds2_genotypes
     ds2_subset["call_genotype_mask"] = ds2_subset["call_genotype_mask"].isel(variants=ds2_idx)
 
     return (ds1_subset, ds2_subset)