[Biojava-l] using phred calls with ChromatogramGraphic produced from ab1 files

[Andrew Farmer]

Hi all-
I have been trying to use the ChromatogramGraphic class to display ABI 
chromatogram data, whilst relating this to alignments of sequences 
called from these trace files with phred. For example, if the user 
clicks a putatively polymorphic base in an alignment viewer, to scroll 
and highlight the region of the ChromatogramGraphic corresponding to the 
ase call. However, I seem to be having some difficulty in establishing 
correspondences between the phred base calls and the information shown 
in the graphic.

As far as I understand what is being displayed by ChromatogramGraphic, 
it is drawing "callboxes" around peaks corresponding to calls that are 
stored by Chromatogram, which in turn is storing information about the 
base calls that was encoded in the ABI file. These tend to differ 
substantially (e.g. in lower-quality areas) from the calls made by 
phred- e.g. an untrimmed phred-called sequence might have 1300 bases to 
the abi-called version's 900 bases. So, I am trying to find some way to 
get the ChromatogramGraphic callboxes to reflect the calls made by phred.

Has anyone else encountered this type of situation before? It appears 
that phred's phd output encodes a trace offset for each of its calls, so 
I would guess that one could conceivably overlay the phred calls into a 
chromatogram produced by the abi parser in order to get the callboxes to 
reflect phred's interpretation of the trace data.

I could be way off-base (no pun intended) in my interpretation, and 
would appreciate any insights from the gurus out there. And if this is 
more or less correct, and there is not yet a canned solution, any advice 
on how to go about coding it in a way that could be contributed back to 
the project would be great.

Thanks in advance
-- 

Andrew Farmer
adf at ncgr.org
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

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