[Bioperl-l] need help in phredPhrap

[neeti somaiya]

Hi,

I am running phredPharp, which runs phred, phrap and polyphred. Please refer
to the "Using a reference sequence" section of this link
http://droog.mbt.washington.edu/poly_doc50.html#REFER.
I am using the reference sequence as described in the link above.
With this I am getting the SNP positions on the contig sequence as well as
on the reference sequence.
Does anyone know if there is some output file which can also give me mapping
between contig sequence and reference sequence?
-- 
-Neeti
Even my blood says, B positive