Is it possible to normalize the number of observed SNPs to the size of the genome a good quality call can be made

Hello, I am trying to use BEAST to infer the ancestry of intra-specific isolates (we have ~200). I currently have a list of SNPs called from illumina sequencing data. Since Im basing my BEAST analysis on these SNPs, is there a way to normalize the number of mutational events observed in each isolate to the size of the genome over which a high quality call is possible? Would this be even necessary? I assume one way of doing this would be to do some bootstrapping, but this would be too PC time consuming