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.
I like the original Mutect a lot and just downloaded second version of MuTect. I've tried it on my exome BAM files aligned in SE and PE modes. Turns out with PE alignments it takes much-much longer to do SNP call (6 days vs less than a day under the same hardware configuration).
Is that due to the local realignment algorithm? Is that expected?
I do understand that this is beta version, just trying to understand and maybe give some feedback.