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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.
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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