use the output of

 bcftools mpileup --annotate 'FORMAT/DP4' --regions-file mybed.bed --no-reference in.bam'

I don't have a full answer but I have a comment that might help. Samtools depth does not do what you are asking in a one and done. It reports chr pos depth/coverage.

I think the first thing you could do would be to split your bams into the forward bam, and reverse bam:

Forward bam:

samtools view -F input.bam > forward.bam

Reverse bam:

samtools view -f input.bam > reverse.bam

Then running samtools depth on the forward and reverse, I'll add the -a flag to make sure positions align:

samtools depth -a forward.bam > forwardDepth.txt
samtools depth -a reverse.bam > reverseDepth.txt
paste forwardDepth.txt reverseDepth.txt > forwardAndReverse.txt

This will give you a format of:

chr    pos1    cov    chr    pos1    cov

Since the positions are aligned you probably only want the chr, pos, cov forward, and cov reverse ( I know this can be piped with the previous step):

awk '{print $1, $2, $3, $6}' forwardAndReverse.txt > forRev_cut.txt
sed -i '1s/^/Chr    Position    ForCov    RevCov' forRev_cut.txt

The sed bit adds a header if you're interested. I do not know a tool for getting the base count at each position off of the top of my head, so I cannot add that. This is why I did not post as an answer, but I do believe this is a good start! Once you find a way to do the next step, you could run it on both the forward and reverse reads individually and get an output from that to see if numbers match up.

Dennis