diff --git a/setup.py b/setup.py
index 5e771f4a1a88e191dd0e523cd73e5c833567c859..473bac645540d254d3f9ed8eb8a836829828373f 100644
--- a/setup.py
+++ b/setup.py
@@ -28,7 +28,7 @@ setup(
         "numpy",
         "pandas",
         "pyBigWig",
-        "pybedtools",
+        "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
         "scipy",
         "seaborn"],
     #dependency_links=["git+https://gitlab.pasteur.fr/bli/libworkflows@744dd79b579577cb6e131653260d7990946be3ad#egg=libworkflows-0.1"],