Pileup Question

[kasthuri]

Hi,

I am having several bam files and I need to do a pileup of each bam's such that all the pileups have the complete hg19 coordinates. 'samtools mpileup' with all the bams misses certain coordinates. Can somebody tell me how to do a pileup of the entire genome. It can have 0 reads when there are no reads at that location. Of course, I can write a script to do this, but is there any shorter way?

Thanks.