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.
MUTECT2 vs MUTECT1
We are using MUTECT to call somatic variants in cancer
thus far we were using MUTECT1
It works fast, however it does not call indels.
New MUTECT2 in GATK 3.5 calls both point mutations and indels.
The only problem that we have with Mutect2 is that it is much slower (20-50 times) than Mutect1.
We tried to parallelize it, but it is still super slow.
Maybe you could help us with this issue?
Thanks in advance