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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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

How to use multiple inputs in MarkDuplicatesSpark

Dear GATK team, the possibility to use multiple inputs in MarkDuplicatesSpark has recently been added.
However I do not fully understand how to define it on the command line as I have not found examples.

With the picard MarkDuplicates you specifies multiple -I options. But in the documentation of MarkDuplicatesSpark the --input option is noted as a List[string] type, how does it work?

By the way, do you have documentation somewhere listing all the variable types with examples? this would be very helpful.

Thanks for your help.

Best Answer


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