diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index cd5fad3a347..da52fe72233 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -314,9 +314,6 @@
     <tool file="gatk/variant_eval.xml" />
     <tool file="gatk/variant_combine.xml" />
   </section>
-  <section name="NGS: Variant Detection" id="variant_detection">
-    <tool file="variant_detection/freebayes.xml" />
-  </section>
   <section name="NGS: Indel Analysis" id="indel_analysis">
     <tool file="indels/sam_indel_filter.xml" />
     <tool file="indels/indel_sam2interval.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 79dcea9ec0a..27c13063cec 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -419,9 +419,6 @@
     <tool file="gatk/variant_eval.xml" />
     <tool file="gatk/variant_combine.xml" />
   </section>
-  <section name="NGS: Variant Detection" id="variant_detection">
-    <tool file="variant_detection/freebayes.xml" />
-  </section>
   <section name="NGS: Peak Calling" id="peak_calling">
     <tool file="peak_calling/macs_wrapper.xml" />
     <tool file="peak_calling/sicer_wrapper.xml" />