comparison of variants between WGS samples

Question

[cocchi.e89]

I never worked on such specific task so there may be a simple solution that I don't know, I need to find the rate of similarity and find out what are the differences between 2 WGS human samples. Let's say I want to know what variants are specific of sample1, what are specific of sample2 and what are shared between sample1-sample2.

I run GATK HaplotypeCaller on them and I have the GVCF results. How can I compare them? Is there any software out there able to find out differences between samples?

Thank you very much in advance for any help!

Answer 1

[harold.smith.tarheel]

VCFtools '--diff' command can be used to compare VCFs for unique and shared variant calls.

[GenoMax]

OP has GCVF's. VCFtool can handle those?