Okay, this question turns out more complex that I thought and it deserves a separate page.

People used SNVMix in the past, from the Original paper and anotherNature paper. However, it seems out of date as they are still focusing on old aligner — MAQ and old pileup format output from samtools

Another post on biostar indicates that both samtools and GATK will do the work.

Okay, let’s take a look at JointSNVMix