Which parameter is reflecting the maximum number of mismatches when using bwa aln - SEQanswers

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btphzxc

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Join Date: Jan 2022

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Which parameter is reflecting the maximum number of mismatches when using bwa aln

01-05-2022, 11:00 PM

I have seen some discussions about this but still cannot confirm the answer.
My question is that if I want to allow 3 mismatches when using bwa aln, I should type in bwa aln -n 3, or bwa aln -k 3, or another code?
Tags: bwa, mismatches

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