Sorry for the slow response, I've been out of town. Short answer: That input is optional and may not be relevant to all cancers, so you may be fine without it. Long answer: I believe we take the frequencies of germline SNPs in the tumor genome and look for large regions where there are no het sites, caused by CN-neutral LOH (aka UPD). You can segment them into discrete regions using CBS, as implemented in the DNAcopy package for R. Plotting on a per-chromosome basis should also make them clearly evident, if they exist. - Chris Miller