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.