If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Consensus sequences

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?


Sign In or Register to comment.