Changes

=== '''Do I have to sort the pedigree file by physical positions? '''  ===

=== '''Do I have to sort the pedigree file by physical positions? '''  ===

A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br>

If you use external reference, 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 specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''  ===

=== '''What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''  ===