error using gatk 3.8 Argument with name '--analysis_type' (-T) is missing

Question

[chenglei1865]

Hi,

Although gatk4 is new, while some softwares are only compatible with <gatk4, I tries to use gatk3.8, but error occurred,

java -jar GenomeAnalysisTK.jar

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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 http://www.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: Argument with name '--analysis_type' (-T) is missing.
##### ERROR ------------------------------------------------------------------------------------------

Could someone help me out? I appreciate it!

[Pierre Lindenbaum]

show us the command line.

[Vic]

This might sound obvious, but have you attempted to google this. After a single google, I found several help posts based around this issue and you can read those and work your way through each issue. Posts like this

However, on Biostars it is better to give more information so people can help you. For example, what was the command you inputted? Were you using Haplotypecaller? Help us to help you.