Is there any best practice for the mouse snp indel vcf files using GATK Mutect2 for mouse whole exome data? For mm10, it seems have several available, for mm39, it seems the newest is from /pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels, 2021 version.
Besides, when dealing with human samples, GATK GetPileupSummaries have gnomad.vcf.gz files to use, as mouse seems do not have this file available. Does it means this steps for mouse can be skipped?
When looking at the papers, most are focus on human genome as reference, does this also means that research are more focus on human species, not on mice, even on mice, more like PDX or CDX model, so most used reference will still be human.
Thanks a lot!
=The tool requires a common germline variant sites VCF, e.g. derived from the gnomAD resource, with population allele frequencies (AF) in the INFO field.