diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b18448fc..dcd71845 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -81,6 +81,46 @@ jobs:
           # https://github.com/coverallsapp/github-action
           fail-on-error: false
 
+  optional_dependencies:
+    name: Optional dependencies
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Test optional dependencies
+        run: |
+          python -m venv env-tskit
+          source env-tskit/bin/activate
+          python -m pip install .
+          python -m bio2zarr tskit2zarr convert tests/data/ts/example.trees ts.vcz > ts.txt 2>&1 || echo $? > ts_exit.txt
+          test "$(cat ts_exit.txt)" = "1"
+            grep -q "This process requires the optional tskit module. Install it with: pip install bio2zarr\[tskit\]" ts.txt
+          python -m pip install '.[tskit]'
+          python -m bio2zarr tskit2zarr convert tests/data/ts/example.trees ts.vcz
+          deactivate
+
+          python -m venv env-plink
+          source env-plink/bin/activate
+          python -m pip install .
+          python -m bio2zarr plink2zarr convert tests/data/plink/example.bed plink.vcz > plink.txt 2>&1 || echo $? > plink_exit.txt
+          test "$(cat plink_exit.txt)" = "1"
+          grep -q "This process requires the optional bed_reader module. Install it with: pip install bio2zarr\[plink\]" plink.txt
+          python -m pip install '.[plink]'
+          python -m bio2zarr plink2zarr convert tests/data/plink/example.bed plink.vcz
+          deactivate
+
+          python -m venv env-vcf
+          source env-vcf/bin/activate
+          python -m pip install .
+          python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz > vcf.txt 2>&1 || echo $? > vcf_exit.txt
+          test "$(cat vcf_exit.txt)" = "1"
+          grep -q "This process requires the optional cyvcf2 module. Install it with: pip install bio2zarr\[vcf\]" vcf.txt
+          python -m pip install '.[vcf]'
+          python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz
+          deactivate
+
   packaging:
     name: Packaging
     runs-on: ubuntu-latest
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index c09be0d8..fcda2cd7 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -38,7 +38,7 @@ jobs:
 
       - name: Install package
         run: |
-          python3 -m pip install .
+          python3 -m pip install '.[all]'
 
       - name: Build Docs
         run: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e7f602e2..11c3c261 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,7 @@
 # 0.1.6 2025-0X-XX
 
+- Make format-specific dependencies optional (#385)
+
 - Add contigs to plink output (#344)
 
 Breaking changes
diff --git a/bio2zarr/core.py b/bio2zarr/core.py
index f526dc9b..723dd2b7 100644
--- a/bio2zarr/core.py
+++ b/bio2zarr/core.py
@@ -1,6 +1,8 @@
 import concurrent.futures as cf
 import contextlib
 import dataclasses
+import functools
+import importlib
 import json
 import logging
 import math
@@ -21,6 +23,26 @@
 numcodecs.blosc.use_threads = False
 
 
+def requires_optional_dependency(module_name, extras_name):
+    """Decorator to check for optional dependencies"""
+
+    def decorator(func):
+        @functools.wraps(func)
+        def wrapper(*args, **kwargs):
+            try:
+                importlib.import_module(module_name)
+            except ImportError:
+                raise ImportError(
+                    f"This process requires the optional {module_name} module. "
+                    f"Install it with: pip install bio2zarr[{extras_name}]"
+                ) from None
+            return func(*args, **kwargs)
+
+        return wrapper
+
+    return decorator
+
+
 def display_number(x):
     ret = "n/a"
     if math.isfinite(x):
diff --git a/bio2zarr/plink.py b/bio2zarr/plink.py
index f864f3a5..76cad279 100644
--- a/bio2zarr/plink.py
+++ b/bio2zarr/plink.py
@@ -1,7 +1,6 @@
 import logging
 import pathlib
 
-import bed_reader
 import numpy as np
 import zarr
 
@@ -11,7 +10,10 @@
 
 
 class PlinkFormat(vcz.Source):
+    @core.requires_optional_dependency("bed_reader", "plink")
     def __init__(self, path):
+        import bed_reader
+
         self._path = pathlib.Path(path)
         self.bed = bed_reader.open_bed(path, num_threads=1, count_A1=False)
 
@@ -175,7 +177,10 @@ def convert(
 
 # FIXME do this more efficiently - currently reading the whole thing
 # in for convenience, and also comparing call-by-call
+@core.requires_optional_dependency("bed_reader", "plink")
 def validate(bed_path, zarr_path):
+    import bed_reader
+
     root = zarr.open(store=zarr_path, mode="r")
     call_genotype = root["call_genotype"][:]
 
diff --git a/bio2zarr/tskit.py b/bio2zarr/tskit.py
index 4dccedaa..112e901a 100644
--- a/bio2zarr/tskit.py
+++ b/bio2zarr/tskit.py
@@ -2,7 +2,6 @@
 import pathlib
 
 import numpy as np
-import tskit
 
 from bio2zarr import constants, core, vcz
 
@@ -10,6 +9,7 @@
 
 
 class TskitFormat(vcz.Source):
+    @core.requires_optional_dependency("tskit", "tskit")
     def __init__(
         self,
         ts_path,
@@ -18,6 +18,8 @@ def __init__(
         contig_id=None,
         isolated_as_missing=False,
     ):
+        import tskit
+
         self._path = ts_path
         self.ts = tskit.load(ts_path)
         self.contig_id = contig_id if contig_id is not None else "1"
diff --git a/bio2zarr/vcf_utils.py b/bio2zarr/vcf_utils.py
index a8b3b551..b51e8ebc 100644
--- a/bio2zarr/vcf_utils.py
+++ b/bio2zarr/vcf_utils.py
@@ -9,10 +9,10 @@
 from enum import Enum
 from typing import IO, Any
 
-import cyvcf2
 import humanfriendly
 import numpy as np
 
+from bio2zarr import core
 from bio2zarr.typing import PathType
 
 logger = logging.getLogger(__name__)
@@ -395,7 +395,10 @@ class VcfIndexType(Enum):
 
 
 class VcfFile(contextlib.AbstractContextManager):
+    @core.requires_optional_dependency("cyvcf2", "vcf")
     def __init__(self, vcf_path, index_path=None):
+        import cyvcf2
+
         self.vcf = None
         self.file_type = None
         self.index_type = None
diff --git a/bio2zarr/vcz_verification.py b/bio2zarr/vcz_verification.py
index 6faf356d..2af708c3 100644
--- a/bio2zarr/vcz_verification.py
+++ b/bio2zarr/vcz_verification.py
@@ -1,9 +1,9 @@
-import cyvcf2
 import numpy as np
 import numpy.testing as nt
 import tqdm
 import zarr
 
+from bio2zarr import core
 from bio2zarr.zarr_utils import first_dim_iter
 
 from . import constants
@@ -146,7 +146,10 @@ def assert_format_val_equal(vcf_val, zarr_val, vcf_type, vcf_number):
         nt.assert_equal(vcf_val, zarr_val)
 
 
+@core.requires_optional_dependency("cyvcf2", "vcf")
 def verify(vcf_path, zarr_path, show_progress=False):
+    import cyvcf2
+
     root = zarr.open(store=zarr_path, mode="r")
     pos = root["variant_position"][:]
     allele = root["variant_allele"][:]
diff --git a/pyproject.toml b/pyproject.toml
index f838e084..17898968 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,16 +17,12 @@ dependencies = [
   "zarr >= 2.17,< 3",
   # Pinning numcodecs due to https://github.com/zarr-developers/zarr-python/issues/2963
   "numcodecs[msgpack]!=0.14.0,!=0.14.1,<0.16",
-  "click",
   "tabulate",
   "tqdm",
   "humanfriendly",
-  # cyvcf2 also pulls in coloredlogs and click",
-  # colouredlogs pulls in humanfriendly",
-  "cyvcf2",
-  "bed_reader",
-  # TODO Using dev version of tskit for CI, FIXME before release
-  "tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python",
+  # cyvcf2 also pulls in coloredlogs and click
+  "coloredlogs",
+  "click",
 ]
 requires-python = ">=3.10"
 classifiers = [
@@ -65,8 +61,21 @@ dev = [
   "pytest-coverage",
   "pytest-xdist",
   "sgkit>=0.8.0",
-  "tqdm"
+  "tqdm",
+  "tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python",
+  "bed_reader",
+  "cyvcf2"
 ]
+# TODO Using dev version of tskit for CI, FIXME before release
+tskit = ["tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python"]
+plink = ["bed_reader"]
+vcf = ["cyvcf2"]
+all = [
+  "tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python", 
+  "bed_reader", 
+  "cyvcf2"
+  ]
+
 
 [tool.setuptools]
 packages = ["bio2zarr"]
diff --git a/tests/test_core.py b/tests/test_core.py
index 5619fd3a..de596d29 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -244,3 +244,14 @@ def test_examples(self, chunk_size, size, start, stop):
 )
 def test_du(path, expected):
     assert core.du(path) == expected
+
+
+def test_decorator_missing_dependency():
+    @core.requires_optional_dependency("non_existent_module", "extras")
+    def test_function():
+        return "success"
+
+    with pytest.raises(ImportError) as exc_info:
+        test_function()
+
+    assert "pip install bio2zarr[extras]" in str(exc_info.value)
diff --git a/tests/test_plink.py b/tests/test_plink.py
index ed62eaf7..21ae557a 100644
--- a/tests/test_plink.py
+++ b/tests/test_plink.py
@@ -1,3 +1,5 @@
+from unittest import mock
+
 import bed_reader
 import numpy as np
 import numpy.testing as nt
@@ -55,6 +57,21 @@ def test_genotypes(self, ds):
             ],
         )
 
+    def test_missing_dependency(self):
+        with mock.patch(
+            "importlib.import_module",
+            side_effect=ImportError("No module named 'bed_reader'"),
+        ):
+            with pytest.raises(ImportError) as exc_info:
+                plink.convert(
+                    "UNUSED_PATH",
+                    "UNUSED_PATH",
+                )
+            assert (
+                "This process requires the optional bed_reader module. "
+                "Install it with: pip install bio2zarr[plink]" in str(exc_info.value)
+            )
+
 
 class TestEqualSgkit:
     def test_simulated_example(self, tmp_path):
diff --git a/tests/test_ts.py b/tests/test_ts.py
index 96be0f3a..80fbe8d5 100644
--- a/tests/test_ts.py
+++ b/tests/test_ts.py
@@ -1,5 +1,6 @@
 import os
 import tempfile
+from unittest import mock
 
 import numpy as np
 import pytest
@@ -93,6 +94,21 @@ def test_simple_tree_sequence(self, tmp_path):
                 "sample_id",
             }
 
+    def test_missing_dependency(self):
+        with mock.patch(
+            "importlib.import_module",
+            side_effect=ImportError("No module named 'tskit'"),
+        ):
+            with pytest.raises(ImportError) as exc_info:
+                ts.convert(
+                    "UNUSED_PATH",
+                    "UNUSED_PATH",
+                )
+            assert (
+                "This process requires the optional tskit module. Install "
+                "it with: pip install bio2zarr[tskit]" in str(exc_info.value)
+            )
+
 
 class TestTskitFormat:
     """Unit tests for TskitFormat without using full conversion."""
diff --git a/tests/test_vcf_examples.py b/tests/test_vcf_examples.py
index 2e7b93b6..7aaed7a3 100644
--- a/tests/test_vcf_examples.py
+++ b/tests/test_vcf_examples.py
@@ -1,6 +1,7 @@
 import collections
 import pathlib
 import re
+from unittest import mock
 
 import cyvcf2
 import numpy as np
@@ -481,6 +482,22 @@ def test_small_example_all_missing_gts(self, ds, tmp_path_factory):
         p1[1] = True
         nt.assert_array_equal(p1, ds2["call_genotype_phased"].values)
 
+    def test_missing_dependency(self, tmp_path):
+        with mock.patch(
+            "importlib.import_module",
+            side_effect=ImportError("No module named 'cyvcf2'"),
+        ):
+            with pytest.raises(ImportError) as exc_info:
+                vcf_mod.convert(
+                    ["tests/data/vcf/sample.vcf.gz"],
+                    tmp_path / "example.vcf.zarr",
+                    worker_processes=0,  # Synchronous mode so the mock works
+                )
+            assert (
+                "This process requires the optional cyvcf2 module. Install "
+                "it with: pip install bio2zarr[vcf]" in str(exc_info.value)
+            )
+
 
 class TestSmallExampleLocalAlleles:
     data_path = "tests/data/vcf/sample.vcf.gz"