diff --git a/src/sv-pipeline/scripts/apply_ncr_and_ref_artifact_filters.py b/src/sv-pipeline/scripts/apply_ncr_and_ref_artifact_filters.py
index a5461c892..e23cfd018 100644
--- a/src/sv-pipeline/scripts/apply_ncr_and_ref_artifact_filters.py
+++ b/src/sv-pipeline/scripts/apply_ncr_and_ref_artifact_filters.py
@@ -89,6 +89,10 @@ def _apply_filters(record, ploidy_dict, ncr_threshold, filter_reference_artifact
         if 'PASS' in record.filter:
             del record.filter['PASS']
 
+    # if filter is . set to PASS
+    if len(record.filter) == 0:
+        record.filter.add('PASS')
+
     # Clean out AF metrics since they're no longer valid
     for field in ['AC', 'AF']:
         if field in record.info: