Mismatch setting for bwa mem ?

Question

[Picasa]

Hi,

Can we set the mismatch number for bwa mem ? And by the way what is the default number ?

Thanks

[Sej Modha]

According to bwa manual

-B INT  Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]

[Picasa]

This is the mismatch penalty for the score but it does not say how many mismatchs are allowed

[Asaf]

Discussed before (see right panel). TL;DR There is no such parameter, you can screen the resulting bam file.