Hello,
I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message:
java -jar GenomeAnalysisTK.jar -T IndelRealigner
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: IndelRealigner
Any help is more than welcome, I cannot find the problem...
Thank you 