duplicated sequence names in generated reference sequences

[thirtyeggs]

The reference sequences from varsim has two sequences (paternal and maternal), and the name is same in the normal sample and the tumor sample. Sometimes, I have to use these reference sequences from which read are generated. When, the normal reads and the tumor reads are mixed up, I have to use the two reference sequence files (normal and tumor), and the sequences in the two files are same. Could you make the sequence names in the reference sequence unique? Thank you for your help in advance.