I am trying to filter the output vcf file from iPyrad in vcfTools, but the file is not recognized. I was told that there are some formatting differences between the iPyrad output vcf and the dDocent output vcf, but I am unsure how to correct the problem. When I filter SNP's with the dDocent vcf file, it works fine, but with the iPyrad output vcf, it filters out all samples and tells me I have no more data left to analyze! When I look at the logfile, it says that the file cannot be recognized. Please advise. Thank you.