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I'm working with SNP calling in a bacterium - I don't have a set of known SNPs, so prior to recalibration, so generate a mask file from all data. My question is, what should I put for the following two options:
because the bacterium is haploid (and I specify --ploidy 1) it seems like these options should be set to zero, as there are no heterozygous loci, but I worry that if I set them to zero, that it won't work as expected. Any advice? I was just setting them to 0.001