--- a/src/filter/Makefile
+++ b/src/filter/Makefile
@@ -2,3 +2,6 @@
 all:
 	$(CC) $(CFLAGS) $(CPPFLAGS) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz $(LDFLAGS)
 
+clean:
+	rm -vf lumpy_filter
+
--- a/Makefile
+++ b/Makefile
@@ -97,6 +97,7 @@
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	$(MAKE) --no-print-directory -C src/filter/ clean
 	#rm -Rf $(BT_ROOT)/lib
 	#rm -f $(BT_ROOT)/src/api/*.o
 	#rm -f $(BT_ROOT)/src/api/internal/*.o