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. 
If you are looking for a good way of separating the variants into those that are shared between both samples and those that are unique to each sample, I would recommend using `vcfeval` from [RTG Tools][1] to do the comparison, as that will correctly deal with representation differences between the two samples (this may not be such an issue if both samples were called jointly or you are only concerned with simple SNPs). For example:

    rtg vcfeval -t your_reference -b sample1.vcf.gz -c sample2.vcf.gz --squash-ploidy --sample sample1,sample2 -o sample-differences

If both of your samples are in a single VCF, just use the same VCF for both -b and -c. The `--squash-ploidy` option will ignore differences in zygosity in the genotypes and match based on shared alleles. In the output directory you will have variants unique to sample1 in `sample-differences/fn.vcf.gz` and those unique to sample2 in `sample-differences/fp.vcf.gz`, and you can get a summary of the composition of those variants using `rtg vcfstats`.

(disclaimer: I work for RTG, but vcfeval is free and awesome)


  [1]: https://github.com/RealTimeGenomics/rtg-tools