diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config
index 39934a4b..7fbcdc4c 100644
--- a/conf/modules/call_repeat_expansions.config
+++ b/conf/modules/call_repeat_expansions.config
@@ -71,6 +71,7 @@ process {
     }
 
     withName: '.*CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP' {
+        ext.args = '--output-type z --multiallelics -both'
         ext.prefix = { "${meta.id}_split_exp" }
     }