Installing on Windows

Sentieon is a command line tool. On windows it runs inside of Cygwin. Cygwin provides a linux like shell allowing you to write scripts in bash to automate your pipeline.

Requesting a license

Open the windows command prompt by seaching for cmd and selecting Command Prompt from the selections available.


Enter the following command:

ping -a localhost

The output should look like this:


The name after the text Pinging is the Fully Qualified Domain Name of you computer. In this example the FQDN is lachesis.GoldenHelix.local.To get the number of cores on your computer run the following command in the same command prompt window.


Include this and your Fully Qualified Domain Name to your account representative and they will be able to issue you a trial license.

Setting up the Cygwin Environment

The first step will be to download the zip file that contains the specially packaged Cygwin version that is designed to run the Sentieon Sentieon is a command line tool. This can be downloaded here:

Once the file has finished downloading, unzip it to a location with plenty of space. It is important to have enough space for the reference sequence as well as the input files that will be sequenced, to begin make sure the install location has at least 50GB of space.

Once the file is unzipped, the unzipped folder should look like this:


The next step is to set up cygwin to run in the unzipped location. Open the cygwin64 folder:


In the cygwin64 folder is a file called Cygwin.bat. This holds the setting we need to change in order for the cygwin program to function properly in this unzipped location. Right click on the Cygwin.bat file and select edit.


This will open up notepad. Next, edit the value after the chdir command so that the path matches the path to the cygwin64 directory. When you are done it should look like this:


Save the file and close notepad. Congrats your cygwin environment is ready to go!

Once the cygwin environment is setup you can open the cygwin command prompt by double clicking on the Cygwin.bat file. Welcome to cygwin.


If you are not familiar with the linux shell there are a couple commands that you should memorize for navigation:

Use these command to navigate to the unzipped Windows_Sentieon folder inside of the cygwin shell. Note that in cygwin you will be able to find the drives connected to your computer in the /cygdrive/ directory.


Downloading the Resources and Tools

In the cygwin shell enter the Secondary-Analysis folder. Inside of the secondary analysis folder there will be two scripts ( and and the variant_calling.ini file used to store the settings used by the script.


Run the script by executing the following command:


The script will start downloading the reference and cygwin tools. This can take some time as the files are quite large.


Once this completes you can use the example script to call variants on a sample following the directions here Creating a Pipeline.