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Bwa Gapped Alignment

bwa aln has the option "-o INT Maximum number of gap opens [1] " Does this mean by default maximum only 1 gap is allowed?

However, I ran BWA by default and I can see lots of my alignment includes say 5bp, 10bp gaps. How to explain this?

thx

bwa
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updated by Manu Prestat Manu Prestat • written by Bioscientist Bioscientist

1 answer

I guess that you can have a single gap of length 10pb. This is still one gap.

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written by Manu Prestat Manu Prestat

ok, i see..One gap can contain many bases....actually my gap can include 20bp as far as I see.

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written by Bioscientist Bioscientist

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