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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

GATK doesn't find the MuTect2 tool?

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    Bhanu Gandham

    Nicola Dick

     

    What you are looking at is a very old version of GATK. Please look at the latest version which has the correct usage examples: https://gatk.broadinstitute.org/hc/en-us/articles/360042476952-FilterMutectCalls

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    Nicola Dick

    Hi there!

    This is the doc I had been trying to work with. It refers to the tutorial I linked in the post above. My problem is, although I installed gatk probably and it runs ( checked it with the command ./gatk --help  as suggested) , I cannot call any tool. In my case I just want to use MuTect2.

    running

    gatk [--java-options "jvm args like -Xmx4G go here"] ToolName [GATK args go here]

    is exactly what I tried in the example above. And I don't find what I need to do differently to execute it.

     

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    David Benjamin

    Nicola Dick Your error message "-bash: gatk: command not found" means that the bash shell doesn't recognize the command "gatk", not that the gatk doesn't recognize the command "Mutect2".  There is indeed no problem with your gatk command other than the fact that you bash shell doesn't know what you mean by "gatk."

    Notice the difference between ./gatk (which worked) and gatk (which didn't).  In the former, you are telling the shell: "run a script called gatk that lives in the current directory."    In the latter, you are telling the shell: "run a script called gatk that lives in one of the directories specified in your $PATH environment variable, such as /usr/bin."

    I suspect that using ./gatk Mutect2 . . . will make everything work, but please let us know if it does not.

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    Nicola Dick

    Hey David!

    Yep, this made it work. Thanks a lot for your explanation! :) 

     

    I have been working with some gatk tools these last days and saw similar, maybe not that trivial things popping up and wonder if this is supposed to be like this.

    For most experienced people here with more background in bioinformatics a lot of things might all be self explanatory. But they might unnessecarily exacerbate the start for beginners from other fields (statistical physics in my case).

    While most articles on here want to serve the purpose of explaining how to use a tool, they use lines of code that might not really work in reality. I usually copied what is said in the instructions just to get error messages. 

    For example in 

    https://gatk.broadinstitute.org/hc/en-us/articles/360036826231-FilterMutectCalls

    the usage example wouldn't work saying that the required argument for the reference was missing. Why doesn't someone include the reference? Because it's too trivial??  For me for example it's not super easy to guess which reference file in which format is wanted when there is no example line of code stating it.

    Not sure if this deserves it's own post :P 

    Many Greetings,

    Nicola

     

     

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    Bhanu Gandham

    I don't think it wasn't included because it was trivial. Its a error on our end and we will fix it. 

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    Nicola Dick

    I see! Thank you Bhanu Gandham

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