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.
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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Calling Somatic Variants without matched normals using GATK.
I am new to the world of bioinformatics. I currently have sequencing data (WES) of about 45 pediatric brain tumor samples (archived FFPE), I am keen on identifying mutational burden and mutational signatures in these samples. I don't necessarily
want to discover a novel mutation and describe it's biological relevance. More use the pattern of mutational signatures to identify the causes of recurrence in tumors. The problem is like with most archived FFPE samples I don't have matched normal tissue. I am looking at the best approach to call somatic variants in these samples. Is Using gnomAD for filtering my best option? Is that a good resource for pediatric tumors? If no then what could be other potential sources for this.
Thank you for your advise.