BWA-MEM PARAMETER TO DETECT MUTATION

Question

[Bhawna]

Hey, I am working with bwa- 0.7.18, in my alignment file I have manually checked for presence of mutation(snp) which is not been picked up by bwa as it shows perfect mapping of 159bp read length. I am working with amplicon data. I have tried to make mismatch score stringent(-B 20 ) but it still isn't picking up that mutation. Can somebody suggest what parameters can I use to make it more sensitive to mutations?

Thanks!

[ATpoint]

Can you show your evidence for this mutation?

[Pierre Lindenbaum]

as it shows perfect mapping of 159bp read length.

show us the CIGAR string and the NM tag