I think my problem deals with the gatk-126.96.36.199.zip file. After I unzip the file I can view the contents; however, no where do I see the GenomeAnalysisTK.jar file? I only see the two gatk-package jar files - listed below.
gatk-package-188.8.131.52-spark.jar and gatk-package-184.108.40.206-local.jar
I'm expecting to find the GenomeAnalysisTK.jar file.
Thank you, this worked. I also made a shell script that also seemed to do the trick, it was simply:
Please use the gatk wrapper script rather than calling the jars directly. See the docs for an explanation of why. Follow the quick start guide here: https://software.broadinstitute.org/gatk/documentation/quickstart
I am facing the same problem like you. How did you create GenomeAnalysisTK.jar script? I have gatk-220.127.116.11 and also only spark and local jar files...I tried to run ./gatk but I only got options on how to run gatk and GenomeAnalysisTK.jar was not created. Please help.