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.
Build a panel of normal for Mutect
I am trying to build a panel of normal for Mutect. After a deep investigation on internet I could not find anything more specific that this:
"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." (from appistry.com/2013/qa-from-the-cancer-genome-analysis-suite-webinar/).
The sentence "From these data, a VCF file is created" is not self explanatory.
Could someone please indicate clearly the command line(s) needed for this procedure? Including (for example) 4 normal samples.
This think this will be extremely useful for the whole community.
Thanks a lot,
Bioinformatician at The University of Melbourne
Royal Melbourne Hospital