Often it is important to pre-process the bams to remove some poor quality reads to help increase the sensitivity of variant calling. Samtools provides functionality for this. For instance, you can remove PCR duplicates:
samtools rmdup in.bam out.bam
Or filter out reads that are not primary alignments (i.e align to multiple locations):
samtools filter -F 256 in.bam > out.bam
Or filter out reads that are not mapped:
samtools filter -F 4 in.bam > out.bam
The 4 and 256 flag is a bitwise flag that can be explained from this website.