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Old 10-20-2009, 01:56 PM   #1
jnfass
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Location: Davis, CA

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Default controlling clipping behavior in bwa 'aln' and 'bwtsw' aligners

How do I control the "soft clipping" behavior in bwa's aln or bwtsw alignment commands (for short and long reads, respectively)? I expect to be able to find alignments that satisfy the edit distance constraints, and clipping defeats that. For example, with a read of 60bp length, bwa aln might me an alignment with the CIGAR string 20S10M1D10M20S ... in other words, there are less than 4% mismatches in the 20 bases involved in the alignment, but 2/3 of the read is clipped off (not involved in the alignment, and does not match the reference). This is not what I want.

Is there something that I'm missing in the options that's controlling the clipping, or do I need to play with the mismatch penalties? Will that even affect clipping?

P.S. In bwa 0.5.4, the bwtsw alignment command is named bwasw, at least in my build.
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Old 01-10-2010, 01:49 PM   #2
elalo
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Default

Hi jfnass,

were you ever able to find a solution or workaround for this? I've just encountered the same issue with my data.
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