To assess copy number variation we merged and analysed the probe-level intensity data from both the Affymetrix and Illumina arrays, identifying 1,610 genomic segments that probably varied in copy number (CNPs) with an estimated MAF of at least 1% of the cohort (see Methods). Further quality control steps yielded a set of reference genotypes for 856 CNPs with a 99.0% mean call rate and 0.3% Mendelian inconsistency—very high accuracy, but still less than that observed from SNP genotyping (Mendelian inconsistency <0.14% in this data set; Supplementary Information). We estimate that the resolution of this analysis to detect CNVs is at a multi-kilobase scale, but not smaller (Fig. 1a).
