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 Genotype Field
I have noticed that when running MuTect, the variant calls in my output always have a genotype of 0/1. I have not seen any 1/1 genotypes, even when the variant allele frequency is 100%.
Are there any instances when MuTect gives a 1/1 genotype for a variant call?