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.
Mutect run in HC + PON mode ?
The Mutect paper said that "To create this filter, we ran MuTect on a set of normal samples as if they were tumor samples without a matched normal sample in STD mode. From these data, a VCF file is created for the sites that were identified as variant by MuTect in more than one normal sample."
We need run Mutect on each normal sample and then integrate all the VCF by users? Or the panel of normal samples can be input to Mutect and a single run in the HC + PON mode gives a single VCF file? How give a set of normal samples as a input of Mutect?