Hi there, i am running the latest version on iPyRAD ( v.0.6.1) using a reference genome.Now this may be a silly question, but how can we know which locus in the .loci file each SNP in the VCF file belongs too? In the old pyRAD (de novo) instead of chromosome position in the vcf file one had the same locus ID as in the .loci file. In iPyRAD /reference mode) I see that in the VCF file for each SNP there is the actual chromosome position (of course!), but in the .loci file each locus is still identified just by a number. I would like to determine which loci to keep by filtering the vcf file, but also create an equivalent .loci dataset containing the same exact loci. At the moment, however, i can't find a way to match the two. Thanks!