Question: Gatk Error Argument With Name 'T' Isn'T Defined
0
Erica Westerman • 10 wrote:
Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy
server, and when I try to run Count Covariates I get the error: ERROR
stack trace
org.broadinstitute.sting.commandline.InvalidArgumentException:
Argument with name 'T' isn't defined. at org.broadinstitute.s
I have looked at the GATK Count Covariates command line, and it looks
to me like the argument with name 'T' is not a place where I need to
input a file, but is where the Count Covariates software information
goes. I get this same error when trying to run Realigner Target
Creator.
I wondered if this might be something that could be simply fixed by
reinstalling the wrappers for GATK, or something along those lines?
Thank you!