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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

Problem Installing and testing GATK-4.1.7.0

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    Tiffany Miller

    Hi Arjun Upadhaya , I think this is an issue with how you set up your path.

    What displays when you run: 

    echo $0  

    What about

    echo $PATH

    Can you confirm the path to the executable? You can navigate to the gatk folder (cd gatk-4.1.7.0) and run ./gatk to execute commands from there while you debug the path issue. I know you did all the work to install the other software required, but running via Docker is also a great way to go.

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    Arjun Upadhaya

    Thank you Tiffany for the suggestions and quick response. I tried few things and the problem was solved.

     

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    Tiffany Miller

    Good to hear. What worked for you (it may help others)? We updated the docs to include a suggestion with adding an alias to your bash profile that points to the gatk python script. 

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    Arjun Upadhaya

    Thank you Tiffany. I should have explained previously what I did. Previously, my path to gatk executable in .bashrc was wrong "export PATH=$PATH:"/home/arjun/Desktop/gatk-4.1.7.0/gatk". I removed "gatk" from the end of path. Previous error "gatk command not found was solved". However, I got another output message "/usr/bin/env:'python':No such file or directory. After some google research I came to know that this message was associated with default python3 installed in my ubuntu 20. I installed python2.7 and made it first choice for the system. Finally, this worked out. Based on my little recent experience, I believe python3 also creates problem in the installation of the gatk4-4.1.7.0. Please correct me if I am wrong. To summarize path to executable 'gatk' and python version were the probable reason for the problem I was facing. Hope this helps to beginners.    

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    Alessio Patamia

    I have a similar problem.

    I use ubuntu 20.04

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