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.
Recommendations for patient derived xenografts (PDX) samples?
Dear fellow bioinformaticians,
I have a large amount of PDX sample to analyze (RNAseq and DNAseq), this means that I need to separate reads that originated from the host genome from reads originating form the xenograft. There are various tools out there but I was wondering if there is GATK approved way to do this? Or if there is not, any high quality recommendations are very much appreciated.