There are several potential problems if you call SNPs from low coverage ancient samples:
- Reference bias
As has been stated here and elsewhere, samtools mpileup does quality recalibration by default. This recalibration does not work very well with aDNA data. To disable this, call snips using -B flag.
- Not enough coverage (duh!)
If you ever need to recover snips from low-coverage genomes, you can use SequenceTools soft written by Stephan Schiffels.