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