REQUIRED for all errors and issues:
a) GATK version used: 4.4.0
b) Exact command used:
gatk Mutect2 \ -R reference.fa \ -I sample.bam \ --germline-resource af-only-gnomad.vcf.gz \ --panel-of-normals pon.vcf.gz \ -O single_sample.vcf.gz
i would like to use GATK-mutect2 for somatic variants calling with mouse tumor tissue. however, i saw multiple posts were about human. and I do find any solution for mutect2 varaints calling in mouse. I want to know, whether in the tumor-only mode, do I need the PoN file and germline-resource, if so, where I can find them? and also, when I perform the BaseRecalibrator, where I can find the mm39 mouse known site (indel + snp)?
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