diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000000000000000000000000000000000..86e9c07b58b1fae4ae873e3fb019e97a3fe0e0f0
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "gatk"]
+	path = gatk
+	url = https://github.com/biopet/gatk.git
diff --git a/gatk b/gatk
new file mode 160000
index 0000000000000000000000000000000000000000..0b73e380436aaa5a41fb3aab97ab651207669f47
--- /dev/null
+++ b/gatk
@@ -0,0 +1 @@
+Subproject commit 0b73e380436aaa5a41fb3aab97ab651207669f47