Hi everyone!

I have a question about BWA-mem parameters.

I know that is usually better to use default ones, but I want to know if someone try to change one or more of them and what are the consequences of changing one of these parameter and if there are some case in which is better to change it and why?

For example, the parameter "-B INT Mismatch penalty. The sequence error rate is approximately: {.75 exp[-log(4) B/A]}. [4]", I've read that if I augment it these affects the variant calling, what if I decrease it?

Does anyone try to change them?

Thank you