These are chat archives for dereneaton/ipyrad
denovo+referenceassembly method. The "GL343210.1" are CHROM names of the unplaced scaffolds in the Anolis assembly, this is a pretty standard naming scheme. The
locus_#CHROM names come from all the reads that did not match to the reference. In the
denovo+referenceassembly method the reads are first mapped to the reference sequence. Then unmapped reads are denovo assembled, and mapped reads are assembled and concatenated to the denovo loci. In the case of the vcf you posted there are only ~1400 unmapped loci, which I assume is a small fraction of the total data. If you don't want unmapped reads you should use the
referenceassembly method, which will throw out all unmapped reads.
-dflag this will generate debug output in the ipyrad_log.txt file. If you can email this to me ill check it out.