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. 
I'm a big fan of vt for this.

http://genome.sph.umich.edu/wiki/Vt#Peek

 #summarizes the variants found in sample.vcf

     vt peek sample.vcf

Also bedtools is very flexible and can work with VCF files so I would use bedtools intersect for this task.

Others have mentioned database joins to be useful too: 
http://www.gettinggeneticsdone.com/2013/11/using-database-joins-to-compare-results.html

