Both samtools view and samtools pileup can take a region as input in the command line, and will only output the region specified. Personally, I think the pileup from samtools looks nicer than the one from GATK. It's apparent immediately when the reads don't match the consensus. And samtools includes where reads start and stop, and which direction reads were going, and puts the coverage right there, so you don't have to count.

You may use simple command-line tools like 'awk' to split the sam alignments before converting to bam files. There is no real utilities to split bam, but you may write your own scripts using Bio::DB::Sam modules to access the bam files and grab the part of data you want.