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.