BWA --> SAM: sequence shown of strand where it maps shown

[Calle]

Hi,

I mapped some Illumina 75x2 reads using bwa (Version: 0.5.8). When I used samtools pileup I noticed that I have loads os variant calls everywhere. Upon further investigation I noticed that the nt-sequence in the sam file is presented on the strans where the read maps and not on the forward strand of the reference (as it should be?).

I have not had this problem with pileups using any other aligner. Is this common behavior for bwa? If so, does anyone know what can be done?
Am I missing something here?

Thanks