BWA inexact matching

Question

[chirag.agrawal.91]

Hi, I have been trying to understand BWA algorithm. I tried running the tutorial as in -

https://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial

bwa aln -t 4 hg19bwaidx s_3_sequence.txt.gz >  s_3_sequence.txt.bwa

bwa samse hg19bwaidx s_3_sequence.txt.bwa s_3_sequence.txt.gz > s_3_sequence.txt.sam

I think these steps only give me exact matches for the queries. Can someone guide me as to how to run for inexact matches. How to set the threshold for inexact matches?

[GenoMax]

Take a look at the `bwa aln options on the help page.

Can someone guide me as to how to run for inexact matches

I assume that means you want to allow for mismatches in alignment?

[finswimmer]

Hello,

to understand the algorithm by BWA I guess you have to first take a look at the code :)

BTW: I think there is no reason to use bwa aln. Use bwa mem instead.

fin swimmer