The various genome scans were integrated using the custom 'pedtool' software. The input to this integration consisted of (a) the raw data, (b) a list of target markers (those from different genotyping labs were kept distinct), (c) cM positions using an integrated genetic map based on NCBI build 35.1 (Duffy, 2006), and (d) a set of data-correction rules, derived from earlier cleaning of the component genome scans, that code for corrections to assumed pedigree structure and the dropping of bad DNA samples.
