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 used the haplotype caller to make consensus sequences. I also tried to make consensus sequences using samtools. What I noticed that samtools put in some places 'N' but the GATK consensus doesn't put N instead it is the same base what reference sequence has. When I checked in using Tablet, I found that samtools consensus sequences were correct. Can you please explain how the consensus sequences are made in gatk when there is no read support for a position. Is it simply assume the reference sequence bases as that position to be correct and put that as a consensus sequence?