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Old 07-23-2010, 04:34 PM   #7
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Originally Posted by Naujv View Post
krobison, thanks! I appreciate your input.

Took your advice and tried bwasw, but sort of ran into a problem with my alignments. My CIGAR string has "S" in them. Found another post where I guess there's a problem with the CIGAR ??

If you have time, I would like your thoughts (and others) regarding using bwasw for reference sequences (not whole genome and not whole chromosomes). Mine are made up of 100 non-overlapping sequences in fasta format.
The "S" character indicates soft-clipping, which is described in the SAM specification. If you still think it is a bug, could you post the SAM record in question?
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