We created 4,000 simulated samples containing a known deletion-1,000 each of a 3-probe deletion, a 5-probe deletion, a 10-probe deletion and a 20-probe deletion. Each simulated sample with deletion size N was generated as follows: (i) choose a random female sample, (ii) choose a random male sample, (iii) randomly permute the order of both the SNP and copy number probes on chromosome X, excluding the pseudo-autosomal regions (this removes natural copy number variation that may occur in either sample), (iv) insert 200 probes from the female sample, (v) insert N probes from the male sample and (vi) insert 200 probes from the female sample. Each simulated deletion used a new random (female, male) pair.
