[Bio-bwa-help] About max edit distance

[YANGKevin <sty...@li...>]

Dear Sir/Madam,
I have tried to use bwa aln with -n 1 -k 0, in order to get some perfect-match reads on the reference. However, in the results, there are still lots of mismatch on some reads. I would like to analyze those reads with 0- or 1-mismatch only. Is it any way to solve this problem?
Best regards,Kevin