diff --git a/README.md b/README.md
index 06afe292ff4b01756841094444d7e020ee394014..2c0e06abffbccc086d71b8a0439b8895fd79b46b 100755
--- a/README.md
+++ b/README.md
@@ -64,7 +64,7 @@ We welcome any kind of contribution, be it merge requests on the code base, docu
 To develop Biopet, Java 7, Maven 3.2.2, and GATK Queue 3.4 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
 
 ~~~
-$ git clone https://github.com/broadgsa/gatk
+$ git clone https://github.com/broadgsa/gatk-protected
 $ cd gatk
 $ git checkout 3.4                              # the current release is based on GATK 3.4
 $ mvn -U clean install
diff --git a/docs/index.md b/docs/index.md
index 39fb7fce5eabd328170ca8019c25c79c856fe8ab..f1445770703faa529b61056c30d5490377c1dc7a 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -64,7 +64,7 @@ We welcome any kind of contribution, be it merge requests on the code base, docu
 To develop Biopet, Java 7, Maven 3.2.2, and GATK Queue 3.4 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
 
 ~~~
-$ git clone https://github.com/broadgsa/gatk
+$ git clone https://github.com/broadgsa/gatk-protected
 $ cd gatk
 $ git checkout 3.4                              # the current release is based on GATK 3.4
 $ mvn -U clean install