How to compare two vcf files of two cultivars?
I am looking for a program that could help to compare two vcf files of two cultivars. I have three vcf files (vcf1, vcf2, vcf3) of SNPs of three different cultivars. The SNPs were called using GATK's UnifiedGenotyper. After stringent filtering with GATK's hard filters, I found approx. 6 millions SNPs in these three cultivars. Now I would like to compare two vcf files of SNPs of any two cultivars (e.g., the combination can be: vcf1/vcf2, vcf1/vcf3 and vcf2/vcf3) to identify common and specific SNPs, and also like to generate venn diagrams between the combinations.
Can anyone suggest me - which tool I can use to identify common and specific SNPs between two cultivars? I do appreciate your help.