samtools mpileup -B or -E

Question

[user230613]

Hi there,

I want to do a variant calling analysis using samtools mpileup and I'm wondering about the meaning of two arguments: -B and -E. I've read the documentation about them, and I've more or less understand whats the meaning of BAQ measure. But I am not quite sure whether I should use -B or -E to adjust the call and make it more accurate, I mean, increase specificity without loosing much sensitivity.

Any help would be appreciated.