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.

Known somatic variants in mice (--known-sites) for BaseRecalibrator in Mutect2

Hi, I need to call somatic variants (SNPs and INDELS) in tumour-normal paired samples in mice using whole genome sequencing data. I would like to use Mutect2 (GATK4) for this. I am in the process of pre-processing the data as shown here: However, for the ‘Recalibrate Base Quality Scores’ step, I am not sure what input to supply for the ‘--known-sites’ option. I could not find known somatic variants for mice in dbSNP, but I did find all germline mutations from the current Ensembl release of mm10, which is the reference I am using- can I use these instead? If not, what would you recommend? Thank you.


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