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 was recently in a very similar situation. I wrote a bash script that finds the "similarity" between two VCF files. Someone might find it useful:

    #!/usr/bin/env bash

    sort -u <(grep -v '^#' $1 | cut -f1,2,4,5) > a
    sort -u <(grep -v '^#' $2 | cut -f1,2,4,5) > b
    comm -23 a b > a_only
    comm -13 a b > b_only
    comm -12 a b > ab
    
    numer=`cat a_only b_only | wc -l`
    denom=`cat ab a_only b_only | wc -l`
    dist=`echo "$numer/$denom" | bc -l`
    sim=`echo "(1-$dist)*100" | bc -l`
    
    echo $sim
    
    # CAREFUL
    rm -f a_only b_only a b ab
<br>
If you put it in `sim.sh` then you can use it like so:

`$ ./sim.sh sample_1.vcf sample_2.vcf`