CNVs were detected in the child/adult case-control, bariatric surgery, SOS sibpair and NFBC cohorts using the cnvHap algorithm (Coin et al., manuscript submitted); this method is based on an Hidden Markov Model which models transitions between copy number states at the haplotype level, improving sensitivity and accuracy by capturing LD information between CNVs and SNPs. The compiled JAR and associated parameter files can be downloaded from http://www.imperial.ac.uk/medicine/people/l.coin/. Sample data from the algorithm applied to the NFBC cohort is illustrated in Supplementary Figure S5a.
