diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index c43969c34cfbfef8b5567a086c533f1b0c3fd6b8..a7c5886fb9ead803baa218944ae92f719c5f8966 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -149,7 +149,7 @@ void BedFile::Open(void) {
 
 // Close the BED file
 void BedFile::Close(void) {
-    if (bedFile != "stdin") delete _bedStream;
+    if (bedFile != "stdin" && bedFile != "-") delete _bedStream;
 }
 
 
diff --git a/src/utils/bedFilePE/bedFilePE.cpp b/src/utils/bedFilePE/bedFilePE.cpp
index 19ab2b1af023ae3a032ce35239c53086fab29097..023a5f5862ab87b41fa181080fbfc4afb193eb4e 100644
--- a/src/utils/bedFilePE/bedFilePE.cpp
+++ b/src/utils/bedFilePE/bedFilePE.cpp
@@ -47,7 +47,7 @@ void BedFilePE::Open(void) {
 
 // Close the BEDPE file
 void BedFilePE::Close(void) {
-    if (bedFile != "stdin") delete _bedStream;
+    if (bedFile != "stdin" && bedFile != "-") delete _bedStream;
 }
 
 
diff --git a/src/utils/bedGraphFile/bedGraphFile.cpp b/src/utils/bedGraphFile/bedGraphFile.cpp
index f3df54026f55a23d7ef3249d265b70e4736d3293..1967a9cd8841a834c240f601e275271c2e493e4a 100644
--- a/src/utils/bedGraphFile/bedGraphFile.cpp
+++ b/src/utils/bedGraphFile/bedGraphFile.cpp
@@ -48,7 +48,7 @@ void BedGraphFile::Open() {
 
 // Close the BEDGRAPH file
 void BedGraphFile::Close() {
-    if (bedGraphFile != "stdin") {
+    if (bedGraphFile != "stdin" && bedGraphFile != "-") {
         if (_bedGraphStream) {
             delete _bedGraphStream;
             _bedGraphStream = NULL ;