This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
h2. Installing GATK