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.
Oncotator: Variant Type SNP/Type of Mutation
I am working on a project with several point mutations. I used oncotator to verify the type of mutation (ie. missense, nonsense, etc) and to see if they were unique mutations or SNPs. I received a variant type of SNP for each and every mutation, does that indeed mean that every mutation was a SNP or is this some type of default. I admit I am new to these databases and need clarification. I am also inquiring whether the indicated type of mutation is accurate...for most the type of mutation was consistent with oncotator, however, I received quite a few discrepancies indicating some of the mutations were splice sites or 3'UTR by oncotator.