![]() ![]() Make sure you choose the correct package for the version of Python you are using. Follow the prompts to properly install the. If you choose to install Anaconda, you may have access to other bioinformatics packages that are helpful to you, and you won’t have to install each package you need. If you are not going to use Conda for anything other than GATK4, you might consider doing the same. We chose to use Miniconda for this tutorial because we just wanted to use the GATK conda environment and did not want to take up too much space on our computer. ![]() Conda provides () about the difference between Anaconda and Miniconda. You will have the option of downloading Anaconda or Miniconda. Choose the correct version/computer you need to download it for. Conda should be easy to install if you follow these steps.ġ) Refer to the () from Conda. Both Conda and Docker are intended to solve the same problem, but one of the big differences/benefits of Conda is that you can use Conda without having root access. The Conda package manager comes with all the dependencies you need, so you do not need to install everything separately. ![]() If you are running GATK4 on a server and/or cannot use the Docker image, we recommend using the Conda package manager as a backup solution. To avoid having to worry about managing these dependencies, we recommend using the GATK4 docker container, which comes with everything pre-installed, as explained (). Some tools in GATK4, like the gCNV pipeline and the new deep learning variant filtering tools, require extensive Python dependencies. For latest documentation and forum click here This information is only valid until Dec 31st 2019. IMPORTANT: This is the legacy GATK Forum Website. ![]()
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