Notice:
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.

Leftover "--allowNonOverlappingCommandLineSamples" in SelectVariants?

Hi guys,
I was subsetting a VCF file with SelectVariants, based on a sample list which contains some additional samples we didn't sequence.

GATK SelectVariants complained about the samples missing from VCF file and the suggested:

##### ERROR 
##### ERROR To ignore these samples, run with --allowNonOverlappingCommandLineSamples

However, I followed the suggestion and got

  ##### 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 'allowNonOverlappingCommandLineSamples' isn't defined.

I can obviously fix this myself as recommended :) but I thought the option was quite convenient, and seemed right to flag this message up as the output suggests to use an option apparently not in place anymore (version 3.5-0-g36282e4)

cheers,
F

Tagged:

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Actually the option is still in place but it is in the wrong case in the error message. Try with --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES instead. We'll fix the error message for the next version.

Sign In or Register to comment.