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?