diff --git a/Makefile b/Makefile
index 5fc4e9b03c233c661c4c3b7cc650783b374dff36..0a1fa06e5dc6f5a208b35ce64c610a0e7f6c726a 100644
--- a/Makefile
+++ b/Makefile
@@ -27,7 +27,6 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/intersectBed \
 		  $(SRC_DIR)/linksBed \
 		  $(SRC_DIR)/maskFastaFromBed \
-		  $(SRC_DIR)/multiBamCov \
 		  $(SRC_DIR)/mergeBed \
 		  $(SRC_DIR)/nucBed \
 		  $(SRC_DIR)/overlap \