pysam IteratorSNPCall output different than the samtools mpileup

[aggp11]

Hi,

I am using pysam to identify variants in our data. I was under the impression that the pysam IteratorSNPCall and SNPCaller both use samtools to identify snps. However when I just run Samtools mpileup to identify snps the output that I get is different

Different in the sense that samtools is calling a lot more positions as potential variants as compared to pysam.

Firstly, does pysam actually use samtools for SNP calling and if yes, then why would the outputs be different?

I would really appreciate if somebody could clarify this.


Thanks,
Praful