Since the path is given, the following post is not relevant. I first wanted to see if the executable is available thtough GATK so I wrote: $ java -jar ~/src/gatk/GenomeAnalysisTK.jarĮrror: Unable to access jarfile ~/src/gatk/GenomeAnalysisTK.jar I removed duplicates with sambamba markdup and I am now on the step for GATK's GenomeAnalysisTK. I am trying to run GATK I understand the first step is to run a realignment.
