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

Can't add to PATH

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    gubrins

    Heys Linda,

    I also had some problems with the PATH.

    When you are trying this: ./gatk --help are you sure you are in that specific folder? If you do ls you should obtain gatk among others. 

    In order to export a path, the command that was working for me was this one (specific case for my exonerate program)

    export PATH=$PATH:/mnt/CIBIO/homes/gabri.mochales/softwares/exonerate-2.2.0-i386/bin/

    I think you have to go until where you have the bin folder, but I'm not really sure, maybe somebody else can confirm it. 

    In relation with the other questions, I understand that you're working from your own computer, right? I think that with those commands you're just executing the programs, but I'm not really sure, as I have them already installed in my server and I just need to call them. 

    I hope I could help at least with the Path!

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    Linda Do

    Thank you!

    Instead of

    ./gatk --help

    I used

    gatk --help

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