Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Download GATK4 required packages in docker container


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    Louis Bergelson


    We don't include every package in our docker image but if you're comfortable with docker it's not hard to make your own image based on ours.  There are at least two ways.

    1.  Run our docker image interactively,

    docker run -it broadinstitute/gatk:

    Then install the tools you want, and then in another shell (outside of the docker instance) on the same machine you can use `docker commit` and save the new image with a new name.  This is the easiest way to get started but it's a pain because if you want to move to a newer version of gatk you have to do it again manually.

    2. The better way which will take a few more steps and some trial and error is to create a new dockerfile that uses our image as the base and add stuff to it.  Basically make a new docker file that starts with importing the GATK docker you want to base your new image on.  

    FROM broadinstitute/gatk:

    RUN: apt-get install bwa ... //your installs here

    Then you can build that docker file and make a new image you can use.   The benefit here is that if you want to rebuild it with a new gatk you can just change the import line.  

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