@dereneaton I'm looking at my .vcf file from ipyrad in vcftools. In ipyrad, I set min_samples_locus to be 237/315 samples, but I have SNPs in my .vcf file that occur in less than 237 individuals. This is the case for about 700/14000 total SNPs in the .vcf file. I used de novo assembly, all reads were 90bp, single end, I filtered out raw reads with any Ns before ipyrad, I set max_Ns_consens to 0. I expected all SNPs to be in at least 75% of my individuals. Why is this not the case? Thanks!!