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Old 04-20-2011, 07:12 PM   #22
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Join Date: May 2010
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Originally Posted by dp05yk View Post
They do not get matched as "A or T or G or C". An N in an input sequence is automatically treated as a mismatch.
It depends which algorithm in BWA you use. I checked for bwasw and there Ns in the input sequence will be replaced by a random base. Therefore, they might not be treated as a mismatch and you will likely get different results when running BWA multiple times.
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