snippy-core outputting more snps?

[hizbullahkhan]

Hello,

I ran 21 isolates of complete genome (each one >1.5Mb) through snippy and then called "snippy-core" with the "snippy-multi" command, and it seemed work and no given error message. I got some output but the number of 'core-snps' generated was more among of each isolate-SNPs (e.g., each of those isolate had 35k - 50k SNPs when aligned to a 3.5Mb reference genome, and the 'core' snps had 182K). How could I get least core-snps (least core-snps as compared each of these isolates) for the complete genome?

Any suggestion about that???

Thank You. Hizbullah