Germline variant calling workflow using GATK
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README.md

variant-call-gatk

This workflow uses GATK to call germline variants in a sequence sample. In two extra VQSR steps for both SNPs and indels common variants are filtered out. This workflow reimplements a study by van der Auwera et al. 2013.

A detailed description can be found on the Cuneiform website. This cookbook installs all necessary tools, downloads all necessary data, sets up Cuneiform, and places the workflow in a predetermined location. The cookbook can be run on any system in a virtual machine. For running the cookbook natively, an Ubuntu 16.04 or higher is required.

Below you find installation instructions for, both, the native and the virtual machine setup.

Prerequisites

Install the following packages:

If you want to set up a VM to test Cuneiform these additional packages are required:

Under Ubuntu you can install the ChefDK by entering on the command line

sudo dpkg -i chefdk_*.deb

Building a VM with kitchen

This section describes how to set up the workflow environment in a Virtual Machine (VM). To do this, it does not matter whether you are running Linux, Mac OS, or Windows. However, if you are running an Ubuntu and want to set up the workflow locally (without creating a VM), see Section Building locally.

To build a VM from this cookbook for the first time, change your git base directory and enter the following:

git clone https://github.com/joergen7/variant-call-gatk.git
cd variant-call-gatk
kitchen converge

You can log into the newly built VM by entering

kitchen login

You can drop the VM by entering

kitchen destroy

Building locally

This section describes how to set up this workflow locally without the indirection of a VM. If you want to try out this workflow in a VM first see Section Building a VM with kitchen.

To install this cookbook locally, create a directory "cookbooks", clone the cookbook into it and run the chef client:

mkdir cookbooks
cd cookbooks
git clone https://github.com/joergen7/variant-call-gatk.git
cd variant-call-gatk
berks vendor ..
cd ../..
sudo chef-client -z -r "variant-call-gatk::default"

Running the Workflow

If you installed the workflow on a VM log into the machine by typing

kitchen login

Execute the workflow script by entering

cuneiform -w /opt/data /opt/wf/variant-call-gatk.cf