Hi folks, I ran ipyrad for GBS using a reference genome and it worked beautifully. Yet, one thing that I don't understand are the "chromosome" names in the vcf file (column #CHROM), which are a mix of actual chromosomes (1-6 in Anolis), NCBI accession numbers (e.g., GL343291.1), and loci in the format "locus_number" (e.g., locus10485; as when running denovo). I was particularly puzzled by these "loci
" loci, since I'm using a reference and I would expect all loci to match to a region of the genome. The reason why this matters to me is that I was using these "names" to match and recover the actual DNA sequences from the .loci file output (i.e., matching SNP ID number to loci ID number in the .vcf, and then loci ID number to sequence in the .loci). Here's one of my vcfs to illustrate what I mean: https://www.dropbox.com/s/3fk3yi0sa1849v5/ortonii_ref_clust75_8x_min17.vcf?dl=0
--Thanks so much!!