I have NGS data from 5 pools of 5 different breeds. My idea is to find a set of SNPs that identify each breed, then a SNP that is present only in one breed and not in the other four. I used several software and filters but when I visualize the results with IGV or Genome Browser the same SNP is present in more than one breed although with a lower number of reads supporting that SNP. Please could you help me to set the filters with Freebayes? any suggestions will be very appreciated.