diff --git a/t1dgrs2_pipeline/v2.0/Dockerfile b/t1dgrs2_pipeline/v2.0/Dockerfile
index 61730d1..9e54050 100644
--- a/t1dgrs2_pipeline/v2.0/Dockerfile
+++ b/t1dgrs2_pipeline/v2.0/Dockerfile
@@ -83,3 +83,4 @@ WORKDIR /data
 RUN chown -R docker:staff /data
 
 ENTRYPOINT [ "/opt/entrypoint.sh" ]
+
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
index 012c0d8..04ac930 100644
--- a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
+++ b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
@@ -459,8 +459,8 @@
             "<inputs.missingness_summary_file>",
             "--remove_file",
             "<inputs.remove_file>",
-            "--output_file",
-            "<inputs.output_dir><inputs.run_id>_export.csv",
+            "--out_prefix",
+            "<inputs.output_dir><inputs.run_id>",
             "--missing_hla_threshold",
             "<inputs.missing_hla_threshold>",
             "--missing_non_hla_threshold",
diff --git a/t1dgrs2_pipeline/v2.0/scripts/generate_file_for_export.pl b/t1dgrs2_pipeline/v2.0/scripts/generate_file_for_export.pl
index 5d7711d..4215898 100755
--- a/t1dgrs2_pipeline/v2.0/scripts/generate_file_for_export.pl
+++ b/t1dgrs2_pipeline/v2.0/scripts/generate_file_for_export.pl
@@ -7,7 +7,7 @@
 my $t1dgrs2_results_file = '';
 my $missingness_summary_file = '';
 my $remove_file = '';
-my $output_file = '';
+my $out_prefix = '';
 my $missing_hla_threshold = 1;
 my $missing_non_hla_threshold = 3;
 
@@ -15,7 +15,7 @@
     't1dgrs2_results_file=s' => \$t1dgrs2_results_file,
     'missingness_summary_file=s' => \$missingness_summary_file,
     'remove_file=s' => \$remove_file,
-    'output_file=s' => \$output_file,
+    'out_prefix=s' => \$out_prefix,
     'missing_hla_threshold:i' => \$missing_hla_threshold,
     'missing_non_hla_threshold:i' => \$missing_non_hla_threshold,
 ) or die("Invalid options");
@@ -44,9 +44,13 @@
 }
 close REMOVE;
 
-# Open output file for writing
-open(OUTPUT_FILE, ">".$output_file);
-print OUTPUT_FILE join(",", "RTI_Accession","GRS2","Missingness_Filter")."\n";
+# Open sample output file for writing
+open(SAMPLE_OUTPUT_FILE, ">".$out_prefix.".csv");
+print SAMPLE_OUTPUT_FILE join(",", "RTI_Accession","GRS2","Missingness_Filter")."\n";
+
+# Open control output file for writing
+open(CONTROL_OUTPUT_FILE, ">".$out_prefix."_controls.csv");
+print CONTROL_OUTPUT_FILE join(",", "RTI_Accession","GRS2","Missingness_Filter")."\n";
 
 # Process t1dgrs2 results file
 open(T1DGRS2_RESULTS, $t1dgrs2_results_file);
@@ -54,21 +58,24 @@
 while(<T1DGRS2_RESULTS>) {
     chomp;
     @F = split("\t");
-    if (!exists($remove{$F[0]})) {
-        my $missingness = "?";
-        if (exists($missing_hla_counts{$F[0]})) {
-            if (
-                $missing_hla_counts{$F[0]} < $missing_hla_threshold
-                && $missing_non_hla_counts{$F[0]} < $missing_non_hla_threshold
-            ) {
-                $missingness = "PASS";
-            } else {
-                $missingness = "FAIL";
-            }
+    my $missingness = "?";
+    if (exists($missing_hla_counts{$F[0]})) {
+        if (
+            $missing_hla_counts{$F[0]} < $missing_hla_threshold
+            && $missing_non_hla_counts{$F[0]} < $missing_non_hla_threshold
+        ) {
+            $missingness = "PASS";
+        } else {
+            $missingness = "FAIL";
         }
-        print OUTPUT_FILE join(",", $F[0], $F[2], $missingness)."\n";
+    }
+    if (exists($remove{$F[0]})) {
+        print CONTROL_OUTPUT_FILE join(",", $F[0], $F[2], $missingness)."\n";
+    } else {
+        print SAMPLE_OUTPUT_FILE join(",", $F[0], $F[2], $missingness)."\n";
     }
 }
 close T1DGRS2_RESULTS;
 
-close OUTPUT_FILE;
+close SAMPLE_OUTPUT_FILE;
+close CONTROL_OUTPUT_FILE;