Hi everyone, I'm feeling really lost with this matter so I'll ask here.
I have RADtags data, I got a vcf that I filtered using vcftools, according to vcftools I have 3,999 "sites" after filtering (which I interpreted as snps) however now that I'm doing an analysis that requires using easySFS I notice the output says I have 30,968 snps (?????) I checked the lines in my vcf and after the header the number of lines also corresponds to 30,968, I understand that each line represents 1 snp but then I don't understand why vcftools interprets 3,999 sites? I tried running vcftools summary filter stats again and again but I keep getting the same, even before filtering I had only 12000 something snps according to vcftools.
Any clue what might be going on here?
I have another dataset that was built and filtered exactly the same as this one and both the number of sites in vcftools and the number of snps in easySFS are the same so I'm really at a loss as to how this is happening
this would not be easy to answer without seeing your VCF file - maybe you could share that VCF and people can take a look at it.