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GATK4 - Available generic command line options and read filters for every tool ?
I am currently trying to set up a pipeline using Mutect2 (GATK 188.8.131.52). I would like to know exactly what this tool is doing with my reads and also whether I am able to supply a multi-threading option. I can not easily find information on that (command line help, online tool documentation or snippets in tutorials).
Is there a way to know for any tool :
- which read filters are applied by default - if there is a support for multi-threading
Thank you very much,