diff --git a/src/batdetect2/cli/data.py b/src/batdetect2/cli/data.py
index cf0698c..4b13224 100644
--- a/src/batdetect2/cli/data.py
+++ b/src/batdetect2/cli/data.py
@@ -137,6 +137,22 @@ def summary(
         "matching names will be excluded from the output."
     ),
 )
+@click.option(
+    "--apply-transforms/--no-apply-transforms",
+    default=True,
+    help=(
+        "Apply any configured sound event transforms to the annotations. "
+        "Defaults to True."
+    ),
+)
+@click.option(
+    "--apply-filters/--no-apply-filters",
+    default=True,
+    help=(
+        "Apply any configured sound event filters to the annotations. "
+        "Defaults to True."
+    ),
+)
 def convert(
     dataset_config: Path,
     field: str | None = None,
@@ -146,6 +162,8 @@ def convert(
     add_source_tag: bool = True,
     include_sources: list[str] | None = None,
     exclude_sources: list[str] | None = None,
+    apply_transforms: bool = True,
+    apply_filters: bool = True,
 ):
     """Convert a dataset config into soundevent annotation-set format.
 
@@ -166,6 +184,8 @@ def convert(
         add_source_tag=add_source_tag,
         include_sources=include_sources,
         exclude_sources=exclude_sources,
+        apply_transforms=apply_transforms,
+        apply_filters=apply_filters,
     )
 
     annotation_set = data.AnnotationSet(
diff --git a/src/batdetect2/data/datasets.py b/src/batdetect2/data/datasets.py
index 7f8ce7b..438c3e5 100644
--- a/src/batdetect2/data/datasets.py
+++ b/src/batdetect2/data/datasets.py
@@ -81,6 +81,8 @@ def load_dataset(
     add_source_tag: bool = True,
     include_sources: list[str] | None = None,
     exclude_sources: list[str] | None = None,
+    apply_transforms: bool = True,
+    apply_filters: bool = True,
 ) -> Dataset:
     """Load all clip annotations from the sources defined in a DatasetConfig."""
     clip_annotations = []
@@ -121,13 +123,13 @@ def load_dataset(
             if add_source_tag:
                 clip_annotation = insert_source_tag(clip_annotation, source)
 
-            if condition is not None:
+            if condition is not None and apply_filters:
                 clip_annotation = filter_clip_annotation(
                     clip_annotation,
                     condition,
                 )
 
-            if transform is not None:
+            if transform is not None and apply_transforms:
                 clip_annotation = transform_clip_annotation(
                     clip_annotation,
                     transform,