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Old 03-15-2011, 04:08 PM   #1
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Location: Colorado

Join Date: Nov 2009
Posts: 1
Default Find long indel from captured gene sequence

This is my first post. Glad to be part of this great community :-)

I am working on a project where my collaborator use the Illumina sequencer to sequence a captured single gene's genomic region (~32,000bp). The idea is to find SNP and other structural variation on this genomic region of DNA from multiple patients. As a control sample, we know that a patient has a 16 bp side by side repeat region. My question is; am I looking at a "long indel" problem? I tried BWA + dindel and did not have much luck!!

Any help would be appreciated
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