diff --git a/.gitmodules b/.gitmodules
index 02da1c44824c83daac94bcfd54ea3f1f9e68c5e2..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "phantompeakqualtools"]
-	path = phantompeakqualtools
-	url = https://github.com/kundajelab/phantompeakqualtools.git
diff --git a/phantompeakqualtools b/phantompeakqualtools
deleted file mode 160000
index 916b09f1b7edba4d47d61ce4930c78fd47e807d9..0000000000000000000000000000000000000000
--- a/phantompeakqualtools
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 916b09f1b7edba4d47d61ce4930c78fd47e807d9