Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
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.

mutsigcv: how to assign categ in coverage table?

santayanasantayana TorontoMember

Hello,

I am trying to figure out how to create my own coverage table for MutSigCV. However, I don't understand the meaning of "categ" in the context of the coverage table. Specifically, how are the labels "transition"/"transversion" assigned to an unmutated base in the genome?

My original hypothesis was that positions were contributing fractionally in a similar way as described for effect, i.e., any given base if mutated would give rise to a transversion 2/3 of the time and transition 1/3 of the time. However if this were the case, categ2 should be twice the value of categ1, categ4 twice categ3, and categ6 twice categ5. There seems to be a trend in this direction in the example file (LUSC.coverage.txt), but there is clearly more going on since the numbers are not exactly double, given the same gene and same "effect". I was hoping someone might be able to clarify.

Many thanks,
Ethan

Tagged:
Sign In or Register to comment.