diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index e128a6574..192d29b73 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -601,8 +601,11 @@ def get_target_events(wildcards):
 
 
 def get_control_fdr_input(wildcards):
-    if wildcards.reference == "main":
+    if wildcards.reference == "main" and wildcards.filter != "nofilter":
         return "results/{date}/filtered-calls/ref~{reference}/annot~{annotation}/{sample}.{filter}.bcf"
+    elif wildcards.reference == "main" and wildcards.filter == "nofilter":
+        # use directly the annotated output, instead of the filtered one
+        return "results/{date}/annotated-calls/ref~{reference}/annot~{annotation}/{sample}.bcf"
     else:
         # If reference is not main, we are polishing an assembly.
         # Here, there is no need to structural variants or annotation based filtering.