diff --git a/src/utils/BamTools/src/api/internal/BgzfStream_p.cpp b/src/utils/BamTools/src/api/internal/BgzfStream_p.cpp
index aba2a0786a095db16c6adf6c8830a3f14bd37f4a..e11032536932e57fdf199aae3435c0caff7cfcfb 100644
--- a/src/utils/BamTools/src/api/internal/BgzfStream_p.cpp
+++ b/src/utils/BamTools/src/api/internal/BgzfStream_p.cpp
@@ -253,15 +253,15 @@ bool BgzfStream::Open(const string& filename, const char* mode) {
     }
 
     // open BGZF stream on a file
-    if ( (filename != "stdin") && (filename != "stdout") )
+    if ( (filename != "stdin") && (filename != "stdout") && (filename != "-") )
         Stream = fopen(filename.c_str(), mode);
 
     // open BGZF stream on stdin
-    else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) )
+    else if ( (filename == "stdin" || filename == "-") && (strcmp(mode, "rb") == 0 ) )
         Stream = freopen(NULL, mode, stdin);
 
     // open BGZF stream on stdout
-    else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) )
+    else if ( (filename == "stdout" || filename == "-") && (strcmp(mode, "wb") == 0) )
         Stream = freopen(NULL, mode, stdout);
 
     if ( !Stream ) {
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index c6c9afd72784bb9ab2604ecd6680831e0ea6b820..43ca3de2bb9a7075df7f064dee1cce0ffe5ed6c1 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -129,7 +129,7 @@ void BedFile::Open(void) {
     
     _bedFields.reserve(12);
     
-    if (bedFile == "stdin") {
+    if (bedFile == "stdin" || bedFile == "-") {
         _bedStream = &cin;
     }
     // New method thanks to Assaf Gordon
diff --git a/src/utils/bedFilePE/bedFilePE.cpp b/src/utils/bedFilePE/bedFilePE.cpp
index f9cd5d2220aad0e9f208aaa582461ad985895e67..e1b84b3f99d39d769f8dd1ab865f19fcba28a491 100644
--- a/src/utils/bedFilePE/bedFilePE.cpp
+++ b/src/utils/bedFilePE/bedFilePE.cpp
@@ -25,7 +25,7 @@ BedFilePE::~BedFilePE(void) {
 }
 
 void BedFilePE::Open(void) {
-    if (bedFile == "stdin") {
+    if (bedFile == "stdin" || bedFile == "-") {
         _bedStream = &cin;
     }
     else {
diff --git a/src/utils/bedGraphFile/bedGraphFile.cpp b/src/utils/bedGraphFile/bedGraphFile.cpp
index 44b87bf9f635b8e64e0b9ef05f4170b082078ae4..df73d8c53f30e12b079ce22ad3c30e06021b4a4c 100644
--- a/src/utils/bedGraphFile/bedGraphFile.cpp
+++ b/src/utils/bedGraphFile/bedGraphFile.cpp
@@ -27,7 +27,7 @@ BedGraphFile::~BedGraphFile() {
 
 // Open the BEDGRAPH file
 void BedGraphFile::Open() {
-    if (bedGraphFile == "stdin") {
+    if (bedGraphFile == "stdin" || bedGraphFile == "-") {
         _bedGraphStream = &cin;
         return;
     }