Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment

Question

[abascalfederico]

Hi,

Reading the documentation it is not clear to me if pysam pileup iterator invokes the BAQ probabilistic realignment in Samtools. I need to compare some results with and without BAQ. Is it possible to do this with Pysam? If not, would it be difficult to change the code to do this? Or is there any other mpileup wrapper available?

Thanks! Federico