Copy number differences between fibroblast and iPSC lines from the same donor were checked using a HMM algorithm implemented in BCFtools/cnv for this purpose 10. In order to distinguish between normal and novel copy number variation as well as to reduce the number of false calls, the program was run in the pairwise mode (bcftools cnv -c <donor> -s <derived>) with default parameters. The CNA calls were filtered to exclude calls with quality score smaller than 2, deletions with fewer than 10 markers, and duplications with fewer than 10 heterozygous markers. Three sets of CNA calls were generated: a more lenient set containing all calls >= 0.2 Mb in length, a set with all calls >= 0.5 Mb and a stricter subset of the previous with calls >= 1 Mb.
