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→Do I always have to sort the pedigree file by marker position?
== Do I always have to sort the pedigree file by marker position? ==
If you use a reference set of haplotypes, you do not have to as long as the external reference is in correct
order. **HOWEVER**, you will probably avoid problems by including markers in the pedigree file sorted in chromosome order.
== What if I specify ''--states R'' where ''R'' exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? ==