diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000000000000000000000000000000000..02da1c44824c83daac94bcfd54ea3f1f9e68c5e2
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "phantompeakqualtools"]
+	path = phantompeakqualtools
+	url = https://github.com/kundajelab/phantompeakqualtools.git
diff --git a/phantompeakqualtools b/phantompeakqualtools
new file mode 160000
index 0000000000000000000000000000000000000000..916b09f1b7edba4d47d61ce4930c78fd47e807d9
--- /dev/null
+++ b/phantompeakqualtools
@@ -0,0 +1 @@
+Subproject commit 916b09f1b7edba4d47d61ce4930c78fd47e807d9