Originally posted by Fabrice ODEFREY
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I don't have a procedure with SOLiD data but would explore this together with you.
First you need to convert the data from color space to sequence space.
Second, convert the sequence to the correct strand. Pindel assume the data is paired-end as illumina so that the reads are facing each other rather than on the same strand.
You may then try my sam2pindel.cpp to extract reads and run Pindel.
Please visit https://trac.nbic.nl/pindel and register as a Pindel user.
Kai
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