Mismatch setting in BWA

[genelab]

Helllo everyone,

I am still comfused how to set the maximum mismatch to 2 when I use "bwa aln", given 75bp reads.

bwa aln -n 2
or
bwa -l 75 -k 2

Any suggestions will be highly appreciated

[genelab]

could anybody help me to answer this question? thanks!

[adamdeluca]

Those are equivalent for 75 bp reads.

[genelab]

Those are equivalent for 75 bp reads.

How about the read length not equal to 75, such as 50 or 100bp?

Thanks for your kindly reply

[adamdeluca]

-n 2 is equivalent to -l READ_LENGTH -k 2