diff --git a/haptools/data/haplotypes.py b/haptools/data/haplotypes.py
index ab58e66c..e243b15d 100644
--- a/haptools/data/haplotypes.py
+++ b/haptools/data/haplotypes.py
@@ -1017,32 +1017,31 @@ def transform(
             [(hap.id, hap.chrom, hap.start, 0, "A", "T") for hap in self.data.values()],
             dtype=hap_gts.variants.dtype,
         )
-        # index the genotypes for fast look-ups of the variant IDs
-        var_IDs = tuple(vID for hap in self.data.values() for vID in hap.varIDs)
-        gts = gts.subset(variants=var_IDs)
-        # initialize arrays needed for proper broadcasting
-        shape = (1, gts.data.shape[1], 1)
-        # and a np array denoting the allele integer in each haplotype
-        allele_arr = np.zeros(shape, dtype=gts.data.dtype)
-        hap_size = {}
-        end = 0
+        # build a fast data structure for querying the alleles in each haplotype:
+        # a dict mapping (variant ID, allele) -> a unique index
+        alleles = {}
+        # and a dict mapping hap ID -> an array with the indices of the hap's alleles
+        idxs = {}
+        count = 0
         for hap in self.data.values():
-            start = end
-            end = start + len(hap.varIDs)
-            hap_size[hap.id] = (start, end)
-        # fill out arrays -- iterate through each haplotype
-        for hap in self.data.values():
-            start, end = hap_size[hap.id]
-            allele_arr[0, start:end, 0] = np.array([
-                int(var.allele != gts.variants[start+j]["ref"])
-                for j, var in enumerate(hap.variants)
-            ])
+            idxs[hap.id] = np.empty(len(hap.variants), dtype=np.uintc)
+            for i, variant in enumerate(hap.variants):
+                key = (variant.id, variant.allele)
+                if key not in alleles:
+                    alleles[key] = count
+                    count += 1
+                idxs[hap.id][i] = alleles[key]
+        self.log.debug(f"Copying genotypes for {len(alleles)} distinct alleles")
+        gts = gts.subset(variants=tuple(k[0] for k in alleles))
+        self.log.debug(f"Creating array denoting alt allele status")
+        # initialize a np array denoting the allele integer in each haplotype
+        # with shape (1, gts.data.shape[1], 1) for broadcasting later
+        allele_arr = np.array([
+            int(allele != gts.variants[i]["ref"])
+            for i, (vID, allele) in enumerate(alleles)
+        ], dtype=gts.data.dtype)[np.newaxis, :, np.newaxis]
         # finally, obtain and merge the haplotype genotypes
-        self.log.info(
-            f"Transforming a set of genotypes of {len(gts.variants)} total variants "
-            f"in {len(self.data)} haplotypes"
-
-        )
+        self.log.info(f"Transforming genotypes for {len(self.data)} haplotypes")
         equality_arr = np.equal(allele_arr, gts.data)
         self.log.debug(
             f"Allocating array with dtype {gts.data.dtype} and size "
@@ -1051,7 +1050,7 @@ def transform(
         hap_gts.data = np.empty(
             (gts.data.shape[0], len(self.data), 2), dtype=gts.data.dtype
         )
+        self.log.debug("Computing haplotype genotypes. This may take a while")
         for i, hap in enumerate(self.data.values()):
-            start, end = hap_size[hap.id]
-            hap_gts.data[:, i] = np.all(equality_arr[:, start:end], axis=1).astype(gts.data.dtype)
+            hap_gts.data[:, i] = np.all(equality_arr[:, idxs[hap.id]], axis=1)
         return hap_gts
diff --git a/haptools/transform.py b/haptools/transform.py
index f5388afc..26e7c5bb 100644
--- a/haptools/transform.py
+++ b/haptools/transform.py
@@ -178,4 +178,5 @@ def transform_haps(
     log.info(f"Writing haplotypes to {out_file_type} file")
     hp_gt.write()
 
+    log.debug("Done!")
     return hp_gt