From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar T. Aykanat, M. Lindqvist, V. L. Pritchard, C.R. Primmer. Journal of Fish Biology 2016, doi:10.1111/jfb.13149 File list and small descriptions of files in deposited to DRYAD Aykanat et al 2016 JFB main code 040916: Main R code to call genotypes of SNPs described in Aykanat et al. using iontorrent raw output in fastq format. SET_FINAL: An R object that contains infromation necessary for calling genotypes. See within the R code for more details. Aykanat et al 2016 JFB supplemntary code 140316: The supplemnetary code which provides some diagnostic figures, and codes to calculate unspecific reads in the iontorrent raw output. This is good e.g. to asses unspecific read number e.g. when you add extra primers to your multiplex panels, or when you design a new panel.