diff --git a/docs/TSD-instructions.md b/docs/TSD-instructions.md
index 8de64f0..e3c130c 100644
--- a/docs/TSD-instructions.md
+++ b/docs/TSD-instructions.md
@@ -8,27 +8,27 @@ In case you are looking to make a full scale test run with the default testing d
 
 # Index
 * [Installation](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#installation)  
-* [Making a clean copy](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#making-a-clean-copy-of-selma-and-the-reference-files-with-the-setup-script)  
-* [Configuring directory paths](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#configuring-directory-paths)  
-* [Reference files](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#reference-files)  
-* [File staging directory](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#file-staging-directory)  
-* [Editing the sbatch file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#editing-the-sbatch-file)  
+	* [Making a clean copy](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#making-a-clean-copy-of-selma-and-the-reference-files-with-the-setup-script)  
+	* [Configuring directory paths](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#configuring-directory-paths)  
+		* [Reference files](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#reference-files)  
+		* [File staging directory](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#file-staging-directory)  
+	* [Editing the sbatch file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#editing-the-sbatch-file)  
 * [Quickstart](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#quickstart)  
 * [Run instructions](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#run-instructions)  
+	* [Locating your input files](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#locating-your-input-files)  
+	* [Preparing the tsv file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#preparing-the-tsv-file)  
+	* [Set the output directory](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#set-the-output-directory)  
+	* [Selecting reference file version](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#selecting-reference-file-version)  
+* [Optional custom interval file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#optional-custom-interval-file-eg-for-exome-calling)  
+
+## Setup checklist
+The following steps are mandatory when you want to run the workflow from scratch:  
+* [Making a clean copy](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#making-a-clean-copy-of-selma-and-the-reference-files-with-the-setup-script)  
+* [Configuring directory paths](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#configuring-directory-paths)  
 * [Locating your input files](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#locating-your-input-files)  
 * [Preparing the tsv file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#preparing-the-tsv-file)  
 * [Set the output directory](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#set-the-output-directory)  
 * [Selecting reference file version](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#selecting-reference-file-version)  
-* [Optional custom interval file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#optional-custom-interval-file)  
-
-## Setup checklist
-The following steps are mandatory when you want to run the workflow from scratch:  
-* [Making a clean copy](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#making-a-clean-copy-of-selma-and-the-reference-files-with-the-setup-script)
-* [Configuring directory paths](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#configuring-directory-paths)
-* [Locating your input files](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#locating-your-input-files)
-* [Preparing the tsv file](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#preparing-the-tsv-file)
-* [Set the output directory](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#set-the-output-directory)
-* [Selecting reference file version](https://github.com/elixir-no-nels/Selma/blob/master/docs/TSD-instructions.md#selecting-reference-file-version)
 
 ## Installation  
 ### Making a clean copy of Selma and the reference files with the setup script