Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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



  • Avatar

    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!

    Comment actions Permalink
  • Avatar
    Linda Do

    Thank you!

    Instead of

    ./gatk --help

    I used

    gatk --help

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk