Finding number of reads and base calls at ~10,000 non-SNPs using BAM file?

Question

[devenvyas]

I am working on paleogenomic data. I have BAM files from two different datasets that were processed/sequenced different. I am trying to look into some relationships between post-mortem damage and batch effects.

I have BAM files for each individual. I have ~10,000 sites where are monomorphic to reference in 1000G + SGDP (so I would think all non-reference calls are error).

I was wondering if anyone could recommend a way where I could probe BAM files to figure out number of total reads at each site as well number of alt reads. Thanks!

(It is also important to me to know where in the read that the base is, but I think that might overcomplicate things for now)