if I have a list of input files, how do I set the output file names?

rcholicrcholic DenverPosts: 68Member

If I put my input files as a list in the file named "input.list", how do I set the output names? or do I just need to set the output folder and the output file names will be automatically named?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,027Administrator, GATK Dev admin

    Depends which tool you are running, but generally speaking you define the main output file name with -o. Be sure to look at the Technical Documentation pages for the tools you want to use; they contain full details about all the different arguments and controls.

    Geraldine Van der Auwera, PhD

  • rcholicrcholic DenverPosts: 68Member

    thanks for your reply, Geraldine. I am using GATK - HaplotypeCaller. If I feed it with a list of input files, do I just need to provide the "-o" with a output folder, something like this "-o /path/to/Var_out/" ?

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