@isaacovercast Hi Isaac, thank you for your response. I am doing 'reference'. Most reads map to the reference, and I see there are bam files for each sample. In the VCF output I see the fasta file I gave as reference in the header, but chromosome IDs are "locus_1", "locus_2", not sequence names in the original fasta. I would like to map SNPs back to their original coordinates in the reference genome.