diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index da52fe72233..55c7d80d1c7 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -208,7 +208,6 @@
     <tool file="phenotype_association/lps.xml" />
     <tool file="phenotype_association/hilbertvis.xml" />
     <tool file="phenotype_association/freebayes.xml" />
-    <tool file="variant_detection/freebayes.xml" />
     <tool file="phenotype_association/master2pg.xml" />
     <tool file="phenotype_association/vcf2pgSnp.xml" />
     <tool file="phenotype_association/dividePgSnpAlleles.xml" />
@@ -319,9 +318,6 @@
     <tool file="indels/indel_sam2interval.xml" />
     <tool file="indels/indel_analysis.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" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 27c13063cec..c2ce858b94d 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -477,7 +477,6 @@
     <tool file="phenotype_association/lps.xml" />
     <tool file="phenotype_association/hilbertvis.xml" />
     <tool file="phenotype_association/freebayes.xml" />
-    <tool file="variant_detection/freebayes.xml" />
     <tool file="phenotype_association/master2pg.xml" />
     <tool file="phenotype_association/vcf2pgSnp.xml" />
     <tool file="phenotype_association/dividePgSnpAlleles.xml" />