diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 8c5932b2208..37ef616a177 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -124,8 +124,10 @@
   	<tool file="regVariation/featureCounter.xml" />
 	<tool file="regVariation/quality_filter.xml" />
     <tool file="regVariation/maf_cpg_filter.xml" />
+	<!--
 	<tool file="regVariation/getIndels_2way.xml" />
 	<tool file="regVariation/getIndels_3way.xml" />
+	-->
   </section>
  <section name="Evolution: HyPhy" id="hyphy">
     <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />