It might be a very stupid question for many of you but, since it's my first variant calling, I didn't figure it out yet. 

I have **mpileup**'ped two bam files from two samples, then I filtered the results with **vcfutils.pl** and called the genotypes with **bcftools** **call**. Now I have a **VCF** file containing what I want, but I managed to analyze differences only between the two samples and the reference (which is an assembly coming from a line that is *different* *from both* *samples*). 

I have the variants between my two samples and the assembly, but what if I want to detect the differences **between** the two samples? I did it with awk / sed / cut and other command line tools but is there maybe a better and more straight-forward way to do that? Perhaps using bcftools? Up to know, I didn't find it. 

Any suggestion appreaciated!  

EDIT: 
I did it with bcftools gtcheck as well, that works fine. I am asking if there are **other** reliable tools to test! 

EDIT 2:
As this post has many views now, I guess it will be useful for everyone to know that I used **bcftools isec** and it worked brilliantly. 
depending on what you're looking for, like simple counts for instance, awk/perl solutions could be enough. if you need a deeper description, `bcftools stats` would give you some interesting details.

if your 2 samples are in a single vcf file I would suggest to split them first

    bcftools view -Oz -c1 -s sample1 joined.vcf.gz > sample1.vcf.gz
    bcftools view -Oz -c1 -s sample2 joined.vcf.gz > sample2.vcf.gz

and then compare them

    bcftools stats sample1.vcf.gz sample2.vcf.gz > joined.stats.txt