diff --git a/tool_dependencies.xml b/tool_dependencies.xml
--- a/tool_dependencies.xml
+++ b/tool_dependencies.xml
@@ -4,7 +4,8 @@
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
-                <action type="shell_command">git reset --hard 9608597d12e127c847ae03aa03440ab63992fedf</action>
+                <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
+                <action type="shell_command">git submodule update --recursive</action>
                 <action type="shell_command">make</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>