Hi there,
Need help for beginner. I have a problem testing gatk-4.1.7.0. I am new to both Linux system and GATK. I am following (gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices) and was able to install BWA, SAMtools, and Picard and successfully test those. To make long story short, I downloaded gatk-4.1.7.0 (Download release :gatk-4.1.7.0.zip) using (github.com/broadinstitute/gatk/releases), uzipped it and placed in Desktop directory. Then, according to the guideline in Getting Started with GATK4 (gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4) section 5 (Install it) I set path for gatk in .bashrc. as given below. The same thing I did for bwa and samtools.
export PATH=$PATH:"/home/arjun/Desktop/gatk-4.1.7.0/gatk"
Assuming that after I set path I can test gatk directly from terminal, I used command
gatk --help
I am getting “Command 'gatk' not found, did you mean:…” and few other lines.
Note. I am using python3 version (Python 3.8.2). Guideline says “You will need Python 2.6 or greater to run the gatk wrapper script”. Also, the java version I am using is “openjdk version 1.8.0_252”. I believe this is java version 1.8 as described in guideline.
Please help me to figure out the problem with installation/testing of gatk. Is the problem related to path issue. If so please help me to figure out.



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