I'm going to call variants with VarScan from a pileup files created with samtools. I realized that there are in general two major possibilities to call variants, pileup as well as mpileup. The VarScan manual says that pileup is for single-sample, mpileup for multi-sample calling. Does that mean that one should use pileup to analyze clones, and mpileup if whole populations have been sequenced? What is the difference between both, pileup and mpileup? What would be the consequences to use the "wrong" pileup?
Moreover, I realized that samtools formerly also had the option pileup. However, pileup was later on deprecated. Thus, would you agree that using mpileup would do the job regardless of the sample?
Thanks a lot in advance!