Are SNPs quality filtered previous to snippy-core?

[alanxelena]

Hi! I have a big question. When running snippy-core are the low quality SNPs called with snippy filtered out? I'm running snippy+snippy-core on 386 E. coli isolates and I'm getting around 86000 core SNPs while publications (with less isolates) talk about 2000 SNPs so I'm wondering if low quality SNPs are actually filtered. Many manu thanks.