BWA best combination of parameters

[wisosonic]

hi all

I am trying to align my illumina's reads using BWA to the human exome
and i am runnig it as defalut parameters ... so i am getting max of 45% of aligned reads ( without any filter on quality or depth )

does anyone have a good combination of parameters for BWA ?

thanks

[2007lab]

Is your reads from whole genome or targeted sequencing?
I am also interested to know these, for SOLID, exome capture samples.