diff --git a/biofuse/cli.py b/biofuse/cli.py
index c468979..80f7bb8 100644
--- a/biofuse/cli.py
+++ b/biofuse/cli.py
@@ -111,7 +111,9 @@ def mount_bgen(vcz_url, mount_dir, basename, access_log_path, **kwargs):
     FUSE process's memory; only ``.bgen`` reads cross the wire.
     ``--no-sample-file`` and ``--no-bgi`` suppress the corresponding
     sidecar; ``--no-header-samples`` drops the sample identifiers from
-    the ``.bgen`` header block.
+    the ``.bgen`` header block. ``--unphased`` ignores the input's
+    ``call_genotype_phased`` field and encodes every variant with the
+    BGEN phased flag clear.
 
     The bcftools-view-style filter / backend / log options are inherited
     from ``vcztools view-bgen``; see ``vcztools view-bgen --help`` for the
diff --git a/biofuse/formats.py b/biofuse/formats.py
index 389ea2c..f547761 100644
--- a/biofuse/formats.py
+++ b/biofuse/formats.py
@@ -129,7 +129,11 @@ def _plink_encoder_factory(reader, opts):
 
 
 def _bgen_encoder_factory(reader, opts):
-    return vcztools.BgenEncoder(reader, embed_header_samples=not opts.no_header_samples)
+    return vcztools.BgenEncoder(
+        reader,
+        embed_header_samples=not opts.no_header_samples,
+        unphased=opts.unphased,
+    )
 
 
 PLINK_SPEC = FormatSpec(
diff --git a/tests/test_bgen_apps.py b/tests/test_bgen_apps.py
index 8c66415..c74660b 100644
--- a/tests/test_bgen_apps.py
+++ b/tests/test_bgen_apps.py
@@ -182,6 +182,19 @@ async def test_no_header_samples_stable_across_opens(
                 data = await trio.to_thread.run_sync(bgen_path.read_bytes)
                 assert data == expected, f"cycle {cycle} differed from reference"
 
+    @pytest.mark.parametrize("unphased", [True, False])
+    async def test_unphased_stable_across_opens(self, tmp_path, fx_small_vcz, unphased):
+        opts = dataclasses.replace(vcztools.ViewBgenOptions(), unphased=unphased)
+        ref_reader = opts.make_reader(str(fx_small_vcz.path))
+        with vcztools.BgenEncoder(ref_reader, unphased=unphased) as ref:
+            expected = ref.read(0, ref.total_size)
+
+        async with _mount_bgen(tmp_path, fx_small_vcz, opts=opts) as (mnt, basename):
+            bgen_path = mnt / f"{basename}.bgen"
+            for cycle in range(3):
+                data = await trio.to_thread.run_sync(bgen_path.read_bytes)
+                assert data == expected, f"cycle {cycle} differed from reference"
+
 
 def _pread_sync(path: pathlib.Path, off: int, size: int) -> bytes:
     with path.open("rb") as f:
diff --git a/tests/test_formats.py b/tests/test_formats.py
index 3a92fb2..96ecb05 100644
--- a/tests/test_formats.py
+++ b/tests/test_formats.py
@@ -313,6 +313,34 @@ def test_embed_default_matches_in_process(self, fx_reader, fx_small_vcz):
         assert data == ref_data
 
 
+class TestBgenUnphasedToggle:
+    """``--unphased`` flows through to ``BgenEncoder(unphased=True)``.
+
+    With the flag set, the encoder must ignore ``call_genotype_phased``
+    and produce the same bytes as an in-process ``BgenEncoder`` built
+    with ``unphased=True`` on the same reader.
+    """
+
+    def test_unphased_matches_in_process(self, fx_reader, fx_small_vcz):
+        opts = vcztools.ViewBgenOptions(unphased=True)
+        with formats.BGEN_SPEC.encoder_factory(fx_reader, opts) as encoder:
+            data = encoder.read(0, encoder.total_size)
+        ref_reader = _open_reader(fx_small_vcz.path)
+        with vcztools.BgenEncoder(ref_reader, unphased=True) as ref:
+            ref_data = ref.read(0, ref.total_size)
+        assert data == ref_data
+
+    def test_unphased_default_matches_in_process(self, fx_reader, fx_small_vcz):
+        opts = vcztools.ViewBgenOptions()
+        assert opts.unphased is False
+        with formats.BGEN_SPEC.encoder_factory(fx_reader, opts) as encoder:
+            data = encoder.read(0, encoder.total_size)
+        ref_reader = _open_reader(fx_small_vcz.path)
+        with vcztools.BgenEncoder(ref_reader, unphased=False) as ref:
+            ref_data = ref.read(0, ref.total_size)
+        assert data == ref_data
+
+
 class TestSpecsRegistry:
     def test_specs_dict_has_both_entries(self):
         assert formats.SPECS == {"plink": formats.PLINK_SPEC, "bgen": formats.BGEN_SPEC}
diff --git a/uv.lock b/uv.lock
index 4657020..c70cd17 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1737,8 +1737,8 @@ all = [
 
 [[package]]
 name = "vcztools"
-version = "0.1.3.dev326"
-source = { git = "https://github.com/sgkit-dev/vcztools.git?rev=main#ae4136fecc8470f359d3152f95d6135330995d53" }
+version = "0.1.3.dev328"
+source = { git = "https://github.com/sgkit-dev/vcztools.git?rev=main#4136ddcf7476e16e2b7d4e0bdaf83bfc3a44b996" }
 dependencies = [
     { name = "click" },
     { name = "humanfriendly" },