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.
Estimate tumor contamination in normal sample
Hello again- I'd like to hear your thoughts about estimating the tumour contamination in a normal sample. (This is useful to know when the matched normal is tissue adjacent to the tumor).
From Estimate cross-sample contamination using GetPileupSummaries and CalculateContamination I see that the combination of getPileupSummaries+CalculateContamination is not appropriate for this task.
However, I see in mutect.pdf, section VII, a proposed strategy for estimating tumor in normal. Do you have any experience/recommendations about it?
Thanks a lot!