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Old 05-25-2012, 05:01 AM   #4
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Location: Berlin

Join Date: Jul 2011
Posts: 156

Yes, basically. I'd really replace the CIGAR with a * though, to make the SAM/BAM file standardized. You might want to check how to decide on which side of the read sequence in the BAM is 5'/3' (in the read, not alignment sense as I understand the SAM spec) however, didn't think about that.
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