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: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11146. 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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