Generate frame-shift data from BAM files

[andrewsssa]

I am analyzing paired-end sequences I obtained from phage display where the inserted fragment is cDNA. Since there are three frames and the chunk of cDNA was inserted randomly, most of the sequences I expect to be out of frame. So, I need to get the frame data.

I have run TopHat to get the BAM files, which nicely shows chromosomal alignments. But does anyone have ideas about how to convert chromosomal position to nucleotide positions or protein sequence?