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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

(How to) Install and use Conda for GATK4 Follow

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    Andrew Brockman

    GATK Team GATK Team: your conda installation link is broken:

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    Stanley Yang

    I installed gatk4 from this site. However, I can not find the "gatkcondaenv.yml" file to configure conda environment. Where is the directory that stores GATK4 jars and the gatk? Thank you!

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    Kathleen Collier

    Hi,

    I freshly installed miniconda3, and then downloaded the latest version of gatk (gatk-4.2.2.0; from https://github.com/broadinstitute/gatk/releases). When I ran 'conda env create -n gatk -f gatkcondaenv.yml', I got nothing but incompatible package warnings as conda tried to resolve them. Ultimately, no environment was generated that I could access and the gatkpythonpackages package was not installed, confirmed through conda list.

     

    The version of miniconda I'm running does work on my computer, as I also run Phyluce from it, but do you have any suggestions as to how to fix this issue?

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