Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GATK 3.8 with MTBseq


I am trying to use GATK with MTBseq and it states that you have to use v3.8 which cannot be installed by conda. I have installed using the following

"conda install -c conda-forge -c bioconda gatk"

Then I downloaded the tar file from your website and used

"gatk-register path-to-downloaded-gatk3.8"

to copy to the conda bath but the command doesn't work. I am a microbiologist so i am not very command line savvy and not sure what I am doing wrong. Any help would be great!




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