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.
BaseRecalibrator without a set of known SNPs
I am putting together a workflow for calling variants in a Mus musculus sub-species. I am a little wary of using the dbSNP as it comes from a separate sub-species. As per the BaseRecalibrator page, it is recommended that one generates a set of known variants by iterating called variants back through the BaseRecalibrator. Would you recommend generating a set of high quality variants by iterating called variants (using HaplotypeCaller) back through BaseRecalibrator for each individual in my sample? Or would you recommend generating a single set of 'gold standard' variants? Do you think that this would make much difference?