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.
Cancer variant calling workflow with mutect and changes/additions to the GATK best practices
I'm working on a cancer variant calling workflow (DNAseq) with MuTect as the variant caller, rather than HaplotypeCaller (due to it's low AF intolerance).
I've gone through the forum and couldn't find a full answer to my inquiry. My question has 2 parts actually:
what changes/additions should I implement in my pipeline/workflow to the GATK Best practices workflow for variant analysis to make it more suitable for cancer variant calling with MuTect, taking into account that I don't have a normal tissue sample, just tumor and an hg19 reference from the bundle:
Is there a difference between the recommended "--known" variants/sites of the GATK's best practices workflow for general variant calling and the one for cancer variant calling with MuTect as the variant caller? Specifically to this article:
Thank you very much in advance,