If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

ContEst: example data

Hi, and first of all, thanks for your time.

While trying to run the first example from your page, with the provided sample files, reference files, etc,I ran into many errors. While I have solved every single one of them, there's an insidious one that I can't get rid of...

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 1.0-6228-gdf95121):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our wiki for extensive documentation
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file
ERROR ------------------------------------------------------------------------------------------

Again, I'm using your provided sample files, but they seem to be badly formatted for the program at hand or it has a bug, or I am doing something wrong. I'd appreciate every single piece of advice.


Sign In or Register to comment.